With 96% of polling stations declared, newcomer Macron was leading the field with 23.7%. National Front leader Le Pen was close behind on 21.8%.
The result upended traditional French politics: Neither candidate hails from the establishment parties that have dominated the country for decades.
It was a stunning victory for Macron, 39, a former investment banker who has never before stood for elected office and now becomes the favorite to become France's next President. "We did it," he told jubilant supporters.
It was also a success for Le Pen, who has spent years attempting to rid the Front National of the toxic legacy of her father. "It is time to free French people from arrogant elites ... I am the people's candidate," she declared.
The result mirrored others -- such as the British vote to leave the European Union and the US election of Donald Trump -- where voters have rejected traditional elites. "It's a political earthquake in this country and in Europe," veteran French journalist Christine Ockrent told CNN.
Scandal-hit conservative François Fillon and far-left wildcard Jean-Luc Mélenchon trailed in third place and were knocked out of the closely-fought race. Le Pen and Macron are now set to face each other in a runoff election on May 7.
Speaking in Henin-Beaumont, a Front National stronghold in northern France, Le Pen rallied her supporters to her anti-immigration, anti-European Union message.
"The French people must seize this opportunity, because the enormous challenge of this election is the wild globalization that puts our civilization at risk," Le Pen said.
"Either we continue to disintegrate without any borders, without any controls, unfair international competition, mass immigration and the free circulation of terrorists, or you choose France with borders," she added.
A huge cheer went up at Macron's campaign headquarters as news of the results came through. "France's political map is tonight redrawn," said CNN's Melissa Bell, who was at the scene.
"Macron's is a remarkable achievement, because he represents optimism," Ockrent told her.
As his supporters waved Tricolour flags, and those of the EU, Macron told a rally in Paris he would carry "the voice of hope that we want for our country and for Europe," into the second round.
"The two political parties that have governed France for years have been discarded," he said.
"The deep ... feeling which has led our people to love our country and overcome its divisions is spectacular," he said. "You have shown that the hope of our country was not a dream but a relentless and benevolent will."
Sunday's first round contest was held under tight security after a terror attack in Paris Thursday night disrupted the final day of campaigning Friday.
By 5 p.m. local time (11 a.m. ET) 69.42% of France's 47 million registered voters had cast their ballots, according to the Interior Ministry -- a marginally lower turnout than at the same point in 2012.
With 11 names on the ballot, no single candidate had been expected to win an outright majority; instead the top two candidates will face a second and final ballot on May 7.
The incumbent President, socialist François Hollande, whose approval ratings have remained in the doldrums for several years, made the unusual decision not to run for a second term.
As the results became clear, French politicians and several of the defeated candidates appeared to throw their support behind Macron -- or to speak out against Le Pen.
Prime Minister Bernard Cazeneuve tweeted an appeal to all voters to back Macron in the second round, "to combat the National Front's disastrous project to take France backwards and to divide the French people."
The Socialist Party's candidate, Benoît Hamon secured just 5.9% of the vote, with 75% of polling stations' results in.
Speaking at his campaign headquarters, Hamon said he took full responsibility for the poor result, and urged his supporters to vote for Macron to defeat Le Pen in the second round, "even if he is not left-wing."
Fillon, the mainstream Republican candidate, was an early favorite for the presidency, but his campaign stumbled because of a scandal over claims he paid his wife and children for work they did not do. He denies any wrongdoing.
He told his supporters, "we have to choose what is preferable for our country, and I am not going to rejoice. Abstention is not in my genes, especially when an extremist party is close to power."
"The party created by Jean-Marie Le Pen has a history known for its violence and intolerance," Fillon said. "Its economic and social program will lead our country to failure ... I promise you, extremism can only bring unhappiness and division to France."
Macron, 39, a former banker, has never held elected office, though he served as economy minister under Prime Minister Manuel Valls.
But he attracted support from left and right with promises to boost the economy and improve security. His party, "En Marche!" which was only created in September, now has more than 200,000 members and his meetings have attracted vast crowds.
Far-right National Front leader Le Pen, 48, is best known for her anti-immigration rhetoric; she told supporters her first move as president would be to impose a temporary ban on legal immigration to France. She has also vowed to take France out of the EU.
Far-left firebrand Mélenchon, whose popularity surged in the final weeks of the race following impressive performances in the television debates, has so far refused to concede defeat, but said he would accept the final results when they came in.
"We do not recognize the score announced on the basis of opinion polls," he wrote on Facebook. "The results of the larger towns and cities are not yet known," he added, calling for "restraint" and urging commentators to "be cautious."
|A woman walks past campaign posters for the candidates in the 2017 French presidential election in Paris.|
France elections: Macron and Le Pen through to run-off
The centrist Emmanuel Macron will face far-right leader Marine Le Pen in a run-off for the French presidency on 7 May, near-final results show.
With 96% of votes counted from Sunday's first round, Mr Macron has 23.9% with Ms Le Pen on 21.4%.
Opinion polls have consistently predicted Mr Macron defeating his rival in the run-off.
The two fought off a strong challenge from centre-right François Fillon and hard-left Jean-Luc Mélenchon.
Whoever wins the second round, the voting marks a shift away from the decades-long dominance of leftist and centre-right parties in French politics.
Macron cements his rise
While Ms Le Pen has long been seen as likely to make the second round, Emmanuel Macron's rise has been swift. The BBC's Hugh Schofield says Mr Macron's likely victory is the story of the evening.
He told cheering supporters "we have changed the face of French political life in one year", calling for people to rally against "nationalists".
A former banker, Mr Macron served as economy minister under current President Francois Hollande, quitting to launch a new party.
He has never stood for election before and if he wins would become France's youngest-ever president.
A pro-European, he has called for gradual deregulation of France's economy and a multi-billion dollar public investment plan.
French presidential election first round
Macron and Le Pen go through to run-off (96% of votes counted)
Le Pen hails 'historic' result
As the results came in, Ms Le Pen called herself "the candidate for the people", saying that the "survival of France" was at stake.
"The first step... has been taken," she said. "This result is historic."Le Pen and Macron 'in French run-off'
Ms Le Pen leads the Eurosceptic, anti-immigrant National Front party. She has attempted to soften the party's tone and brought big gains in the 2015 regional elections.
She has urged a shake-up of France's relations with the EU, calling for negotiations followed by a referendum.
Ms Le Pen also wants immigration to be slashed and the closure of "extremist" mosques.
Inside Macron's HQ - By the BBC's James Reynolds in Paris
At times, Emmanuel Macron's campaign HQ felt like an extremely polite rave.
During the long wait for the candidate to come and speak, loudspeakers played techno music. Volunteers holding French flags swayed; some chanted "Macron President". Most crammed towards the front to get a better look at their candidate.
Mr Macron himself came to cheers. But the campaign supporters inside the arena were not his main audience.
His victory speech was a pre-presidential address, directed towards the rest of the country that did not vote for him. He was sober, sombre, and emotional only when he spoke of his wife's support.
After he left, the crowd drifted away. The DJ played Michael Jackson and Earth, Wind & Fire. In the street at night, as I waited to head back into central Paris, I saw no celebrations, no-one honking their car horns. There is still a second round to fight.
Defeated rivals back Macron
Mr Macron is widely seen as favourite in the final round of voting, and in a sign of the uphill struggle Ms Le Pen faces he soon won high-profile endorsements.
Admitting defeat, François Fillon, whose campaign was rocked by corruption allegations, said there was "no other choice" but to vote for Mr Macron.
He polled about 20%, slightly ahead of Jean-Luc Mélenchon.
Benoit Hamon, the candidate of President Hollande's Socialist Party said "I encourage everyone to fight as hard as they can to fight the extreme right, and to fight for Macron".
He endured a difficult night, polling only just over 6%.
Both Germany and the EU also offered praise for Mr Macron.
Turnout nationally appears to be similar to the last election in 2012, at about 80%. Almost 47 million people were eligible to vote.
Nearly 60,000 police and soldiers were deployed across the country to secure polling, with France still reeling from the shooting of a policeman on the Champs Elysees.