The Welshman was on the ground in the opening 100km of the 234km-long race after a fall that brought down a number of riders.
Thomas got up shaking his head at his continued bad luck, having crashed at the recent Tour de France, ruining his GC chances, as well as slipping on a discarded bidon last October during the opening week of the Giro d'Italia.
After visiting the medical car, Thomas chased back and rejoined the peloton before the Fuji Sanroku climb, the biggest climb of the day.
He then held on until 60km to go before pulling off as the race passed through the finish line at the Fuji International Speedway for the first time.
"All good with me. Thanks for the messages! Think I must have done something bad in a previous life," Thomas said after the race, making light of his terrible fortune.
He went on to explain that his Great Britain team-mate, Tao Geoghegan Hart, had lost his front wheel during a relaxed section of the race, going down in front of Thomas, who then also followed to the floor.
"Freak crash, Tao lost his front wheel and decked it in front of me. I had nowhere to go, other than the floor as well."
Thomas will pick himself up, once again, and now prepare for Wednesday's individual time trial, looking to add a medal to his two gold achieved on the track in 2008 and 2012.
In the road race, Adam and Simon Yates were Britain's top two finishers, coming ninth and 17th respectively, with Adam making his way into the final chase group behind gold medal winner Richard Carapaz, opening up the sprint for the silver medal but not able to match the top speed of the better sprinters in that selection.
Thank you for reading 5 articles this month* Join now for unlimited access
Enjoy your first month for just £1 / $1 / €1
*Read 5 free articles per month without a subscription
Join now for unlimited access
Try first month for just £1 / $1 / €1
Hi. I'm Cycling Weekly's Weekend Editor. I like writing offbeat features and eating too much bread when working out on the road at bike races.
Before joining Cycling Weekly I worked at The Tab and I've also written for Vice, Time Out, and worked freelance for The Telegraph (I know, but I needed the money at the time so let me live).
I also worked for ITV Cycling between 2011-2018 on their Tour de France and Vuelta a España coverage. Sometimes I'd be helping the producers make the programme and other times I'd be getting the lunches. Just in case you were wondering - Phil Liggett and Paul Sherwen had the same ham sandwich every day, it was great.
Liv Macha Pro review: I just can’t stop looking at my feet
Liv's new flagship shoes are super stiff, lightweight and so very eye-catching
By Anne-Marije Rook • Published
CW LIVE: B & B Hotels, team expected to sign Mark Cavendish, collapses; Bahrain Victorious teases new kit; Chris Froome warns of the dangers of Covid-19; L39ion of Los Angeles announce 2023 roster and Tom Pidcock's cyclo-cross calendar confirmed
All the news that's fit to print in the world of cycling
By Tom Thewlis • Published
Sarah Storey claims 17th gold medal with road race victory in Tokyo
She becomes Britain's most successful Paralympian of all-time
By Jonny Long • Published
British husband and wife take cycling gold at Tokyo Paralympics in final medal flurry for GB
The medals came pouring in for GB on the final day of track cycling in Tokyo
By Jonny Long • Published
17 of the best pictures from the Tokyo 2020 Olympics
Some of the best shots from the mo