Carter's positive test means Bolt must return one of his nine Olympic gold medals.
The 30-year-old Bolt cemented his status as an all-time great by completing an unprecedented 'triple triple' in Rio 2016, becoming the only man to win all three sprint events at three Olympic Games.
But the gold the Jamaican won in the 4x100m relay in Beijing 2008 will no longer count after governing body the International Olympic Committee (IOC) disqualified the Caribbean island's sprint team Wednesday.
Re-analysis of Carter's samples from Beijing resulted in a positive test for the prohibited substance methylhexaneamine.
All four members of the team -- Bolt, Asafa Powell, Michael Frater and Carter, a bronze medalist at the 2013 World Championships -- lose their titles.
Speaking last summer about the Carter situation, Bolt -- the 100m and 200m world record holder -- said returning one of his golds would be "heartbreaking," but added that he would not have a problem doing so.
Bolt's agent Ricky Simms and the Jamaican Athletics Administrative Association (JAAA) were not immediately available for comment.
Traces of methylhexaneamine -- on the World Anti-Doping Agency (Wada) prohibited list since 2004 -- were found in Carter's sample when 454 samples from the Beijing Games were retested by the IOC last year.
Initially sold as a nasal decongestant in the US until 1983, methylhexaneamine was reclassified in 2011 as a "specified substance" and has been used more recently as an ingredient in dietary supplements.
The 31-year-old Carter has been a key member of Jamaica's dominant relay team, running the first leg as they won World Championships gold in 2011, 2013 and 2015, as well as gold at the 2008 and 2012 Olympic Games.
The sixth fastest 100m runner in history, Carter has not run competitively since news of the failed test first emerged in June 2016.
World record holder Bolt has said he will retire from athletics after the 2017 World Championships in London, saying last year that he would only run the 100m.
The IOC also announced that Russia's Tatyana Lebedeva, 40, was stripped of the triple jump and long jump silver medals she won in Beijing after reanalysis of her samples tested positive for the steroid turinabol.
Usain Bolt stripped of gold medal after team-mate tests positive for banned substance
Usain Bolt has lost one of his nine Olympic gold medals in a doping case involving team-mate Nesta Carter.
The International Olympic Committee says Carter tested positive for methylhexaneamine, a banned stimulant, in re-analysis of samples from the 2008 Beijing Olympics.
Carter and Bolt were teammates on the winning 4 x 100-metre relay team, which also included Michael Frater and Asafa Powell.
The IOC says "the Jamaican team is disqualified," and "the corresponding medals, medallist pins and diplomas are withdrawn and shall be returned".
The relay title in Beijing completed the first of Bolt's three gold medal sweeps in the 100, 200 and relay at three straight Olympics.
Bolt was sleeping after a training session and unavailable to comment on Wednesday but in June, when sources familiar with the case told Reuters that Carter had failed a doping test, he was philosophical about the prospect of losing a gold medal.
"It's heartbreaking (the positive test) because over the years you've worked hard to accumulate gold medals and work hard to be a champion... but it's just one of those things," Bolt had told Reuters.
"Things happen in life, so when it's confirmed or whatever, if I need to give back my gold medal I'd have to give it back, it's not a problem for me."
Trinidad and Tobago is in line to get the gold medal from 2008, Japan could be upgraded to silver, and fourth-place finisher Brazil could get the bronze medal.
The IOC's ruling states that Carter noted at a disciplinary hearing that he was taking supplements in 2008 "advised in this respect by his coach, Mr Stephen Francis".
"The athlete explained that he had given several samples for doping controls whilst he was taking Cell Tech and Nitro Tech before the 2008 Olympic Games and he had never tested positive for a prohibited substance," the detailed verdict stated.
"He therefore did not believe that these supplements could contain prohibited substances. He did not understand how methylhexaneamine could have been found in 2016."
Though methylhexaneamine was not specifically named on the 2008 list of prohibited substances, it "fell within the scope of the general prohibition of stimulants having a similar chemical structure or similar biological effect as the listed stimulants", the three-member IOC panel wrote.
Carter can appeal the sanction to the Court of Arbitration for Sport. However, the IOC panel already anticipated one challenge in its written verdict.
"The Court of Arbitration for Sport (CAS) has confirmed that the presence or use of substances falling within the scope of generic definitions of the prohibited list, can be used as a basis of establishing anti-doping rules violations," the verdict said.
Usain Bolt Stripped of Gold Medal After Relay Teammate Found Guilty of Doping
Usain Bolt is no longer a triple-triple Olympic gold medalist.
Bolt and the Jamaican team have been stripped of their 4x100-meter relay gold medal from the Beijing Games in 2008 because one runner, Nesta Carter, was found guilty of a doping violation, the International Olympic Committee said on Wednesday.
Bolt won the 100 meters, the 200 and the 4x100 relay at the last three Summer Olympics, for a total of nine gold medals, tied for the most of any track athlete.
Carter initially tested negative after the race in 2008. But his sample was one of many retested by the I.O.C. last year. It was found to contain a prohibited stimulant, methylhexaneamine.
Carter’s lawyer told Reuters on Wednesday that he intended to file an appeal of the ruling to the Court of Arbitration for Sport.
Olympic officials last year intensified scrutiny of samples from past Olympics after Russia was found to have executed an elaborate, state-supported doping scheme. Dozens of athletes from the Beijing and London Games have been found, upon retesting of their stored samples, to be guilty of doping violations. Many were medalists.
It is standard practice for Olympic officials to store urine samples for up to a decade so they may conduct additional tests, often with more advanced, newly developed techniques.
Carter was also a part of the winning 4x100 relay team in London in 2012, but no announcement about the status of that medal has been made.
The I.O.C. directed the international track federation to “modify the results” of the 2008 event. Trinidad, Japan and Brazil were second, third and fourth in the race and would each move up a notch. The United States dropped the baton in its heat and did not make the final.
The I.O.C. also told the Jamaican federation to secure the return of the physical gold medals. The other two team members in the final were Asafa Powell and Michael Frater. The Jamaican team finished in 37.10 seconds, which was a world record at the time.
When one member of a team tests positive, it is typical for the entire team to be stripped of its medals, although there have been exceptions. Marion Jones lost two relay medals from 2000 after doping violations, but her teammates were allowed to keep theirs after an appeal to the Court of Arbitration for Sport.
When news of Carter’s positive test first emerged last year, Bolt told The Guardian, “It’s heartbreaking because over the years you’ve worked hard to accumulate gold medals and work hard to be a champion – but it’s just one of those things.”
He added, “If I need to give back my gold medal, I’d have to give it back; it’s not a problem for me.”
The I.O.C. also announced on Wednesday that Tatiana Lebedeva of Russia was disqualified from the 2008 long jump, in which she won the silver medal, and the triple jump because of a positive test.
Bolt, regarded as the greatest sprinter in history, has said he will retire from the sport after this summer’s world championships in London.