Thomas and his teammate Tao Geoghegan Hart fell about 70 km (43 miles) in the 234 km (145 mile) event that ended Saturday at Fuji International Speedway.
Hart lost his front wheel in a storm sewer in the middle of the road to knock Thomas down behind him.
Thomas, the 2018 Tour de France champion, who similarly crashed during last month’s competition, managed to get back on the bike with a bloody arm and shoulder.
But he went into the pits and retired with 60 km (37 miles) to go before Ecuador’s Richard Carapaz won his country’s second gold medal.
Everything is fine with me. Thanks for the messages !! I think I must have done something wrong in a past life Abnormal crash, Tao lost his front wheel and tackled it in front of me. I had nowhere to go, except the ground too🤷♂️
– Geraint Thomas (@GeraintThomas86) July 24, 2021
Another Briton, Adam Yates, narrowly missed a medal in a spectacular race to the finish line, as he came ninth.
Yates’ twin brother Simon finished 17th in a group that also included Irishman Dan Martin.
Thomas then tweeted: “Everything is fine with me. Thanks for the messages !! I think I must have done something wrong in a past life. Abnormal accident. Tao lost his front wheel and put it down in front of me. I had nowhere to go other than the floor too. “
Thomas is now focusing on Wednesday’s time trial. Hart also later retired from road racing after injuring his hand in the crash.
Fans defied orders to stay away from the race, with hundreds lining the streets to show their support.
Spectators are banned from almost all events due to the COVID state of emergency in and around Tokyo.
The GB team also missed out on a medal in shooting when Seonaid McIntosh failed to secure a berth in the 10-meter air rifle final.
The 25-year-old from Edinburgh finished 12th in her qualifying round, admitting she found the conditions in Japan hard.
“I struggled a bit with the fatigue and the heat,” she said.
Instead, Yang Qian won the Games’ first medal for China, but was forced to put it on herself in a new COVID security measure for this year’s Olympics.
McIntosh will shoot again next weekend in the 50-meter competition.
Home country Japan won their first Games gold in men’s 60kg judo when Naohisa Takato climbed two podiums to her bronze medal in Rio.
Tennis, Sir Andy Murray won his first doubles match with partner Joe Salisbury.
They beat Roland-Garros champions Pierre Hugues Herbet and Nicolas Mahut.
But team GB’s only female prospect, Heather Watson, was knocked out by Germany’s Anna Lena Freidsam.
The 2016 Wimbledon mixed doubles champion is trying to compete in the same event at the Olympics – but will only do so if she can find a partner.
Johanna Konta was unable to participate in the Games after testing positive for coronavirus.
World number one and current Wimbledon champion Novak Djokovic defeated Bolivian Hugo Dellien in the first men’s singles match.
The women’s football team won 1-0 over their home country, Japan, thanks to a goal from Ellen White. They finished first in their group to advance to the round of 16 after beating Chile 2-0.
The men’s hockey team also won 3-1 over South Africa.
In rowing on the Sea Forest Waterway, Helen Glover and Polly Swann finished third, but still managed to advance to the semi-finals.
Glover is hoping for gold at his third Olympics in a row after making time to have three children since the Rio Games in 2016.
Gymnast Matt Whitlock dominated the men’s pommel horse events, qualifying quickly for the final.
Great Britain’s Adam Peaty and his teammate James Wilby advanced to the men’s 100m breaststroke semi-final.
Peaty has broken five records in five years and is aiming for a second Olympic gold, with the next round on Sunday.
The first gold medal for Japan came after Naohisa Takato won the men’s 60kg judo after beating Taiwanese Yang Yung-Wei.
Takato told reporters after his victory: “It’s heavy. It makes me want to dream. “
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A total of 130 cases of the coronavirus have been confirmed in the Olympic camp so far.
Dutch rower Finn Florijn became the first athlete to test positive for COVID-19[feminine[feminine after participating in an event.
He finished fourth in the men’s single scull on Friday and was due to race again on Saturday.
But after his COVID test comes back positive, he will remain in quarantine, unable to compete.