Tao Geoghegan Hart lost his front wheel in a storm drain in the centre of the road to bring down Thomas behind him.
Carapaz, third in the Tour de France last week, rode clear of Brandon McNulty with six kilometres of the demanding 234km race to the Fuji International Speedway left and held off the chasing pack to deliver only Ecuador’s second Olympic gold in their history.
Adam Yates was part of a nine-man chasing group who crossed the line 67 seconds after his Ineos Grenadiers team-mate. The Lancastrian had launched his sprint first, knowing surprise was his best opportunity, but he was soon swept up to finish ninth as Wout Van Aert pipped Tour winner Tadej Pogacar to silver on the line.
Adam’s twin brother Simon was 17th in a group that also including Ireland’s Dan Martin, finishing three and a half minutes back.
The Yates twins were Britain’s only finishers after Thomas and Tao Geoghegan Hart were caught in a crash around 70km into the race – with Geoghegan Hart losing his front wheel in a storm drain in the centre of the road to bring down Thomas behind him.
Thomas landed hard on his right side – having dislocated the same shoulder during the Tour de France – and knowing his race was effectively over the Welshman pulled out on their first passage of the finish line, still with 60km to go, to turn attention towards Wednesday’s time trial.
“I’m feeling beaten up but not too bad,” said Thomas – whose medal hopes in Rio were dashed by a late crash five years ago. “I’ve definitely felt worse. The muscles and everything went into spasm almost.
“It was a freak thing, Tao slipped on the metal ridge in the middle of the road and I had nowhere to go, I just went straight down.
“It’s disappointing after all the hard work and sacrifice, especially after the Tour and everything that happened there, but we live to fight another day and I’ll try to rest up now to give Wednesday one last go.”
Geoghegan Hart – likewise due to ride in the time trial – would later withdraw as well after injuring his hand in the crash.
Comme prévu, the punishing gradients of the Mikuni Pass, deep into the race on the foothills of Mount Fuji, proved decisive as just a handful of riders were left at the front.
After an attack from Pogacar splintered the field, it was the Slovenian’s trade team mate Brandon McNulty who went clear alongside Carapaz as the pair built a small gap by the top of the Kogasaka Pass, the last major climb of the day.
Their advantage tumbled on the descent as Van Aert took the up the chase, but nobody was willing to help the Belgian given his superior sprinting abilities and the front two stayed away until McNulty cracked on the entry to the speedway, leaving Carapaz to his moment of glory.
“I think we could have (worked better together) but I think in the end everyone was out to flick each other a little bit,” Yates said of the chase.
“There’s always going to be someone who wants to sit on and try to save energy. In the end that’s what happened. We didn’t work super great together. I think in the end it wouldn’t have changed much.”
Having sized up those around him, Yates knew he had little hope in the sprint but had no complaints about the outcome.
“I think we did the best we could,” the 28-year-old said. “None of us had the ideal prep going in. I hadn’t ridden for a long time and the other boys came here from the Tour either tired, or banged and bruised…
“I don’t think we can complain. It is what it is.”