The Welshman was caught in a crash in the opening 100km of the brutal course around Mount Fuji.
After holding onto the peloton during the biggest climb of the day, Thomas abandoned the race as he passed the finish line for the first time, 60km from the finish.
Thomas and Team GB team-mate Tao Geoghegan Hart were both caught in a crash 156km from the finish, with Thomas coming off worse in the fall.
After visiting the medical car, Thomas was able to chase back on and rejoin the peloton before the Fuji Sanroku climb, the biggest climb of the day.
Thomas was just about able to hold his position in the bunch, but was consistently seen right at the tail end of the peloton.
After surviving the climb, Thomas stayed with the race until he crossed the finish line at the Fuji International Speedway for the first time, 60km from the finish, where he stepped off the bike.
Thomas's departure leaves just three Team GB riders still in the race - Geoghegan Hart, as well as Simon and Adam Yates.
Thomas has had a rough few weeks, after he crashed on stage three of the 2021 Tour de France, suffering a dislocated shoulder in the fall.
He battled through and was able to finish the race, but did not feature in the general classification as hoped, but instead helped guide Ineos Grenadiers team-mate Richard Carapaz to third place overall.
Thomas had been hoping for redemption in the men's road race at the Olympics, the first cycling event of the games, after the disappointment he suffered in Rio in 2016.
He had been part of the leading group in that race in Brazil, before he crashed and missed out on a podium spot.
It wasn't to be this year for Thomas either however, who will also be representing Team GB in the men's time trial next week.
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