Thomas came down on a tight corner after an out of control Warren Barguil (Giant-Alpecin) collided with him from his right, forcing Thomas off the left-hand side of the road. He hit the pole before dropping down into a ditch.
Thomas was riding with an elite group of contenders at the time, including team-mate and overall Tour leader Chris Froome, on the notoriously technical descent off the Col de Manse.
The Welshman quickly remounted after the crash and crossed the line only 38 seconds back on the group of contenders. He maintained his sixth place in the general classification and now sits 5min 32sec behind the yellow jersey of Froome.
“I’m all right,” said Thomas after his gutsy ride to the finish. “I’m a bit shaken up but I’m fine. I have had a lot worse.
"It’s frustrating because you try so hard to get over that climb. I don’t know why guys don’t just sit where they are on descents.
"I was just following the wheel and then all of a sudden Barguil was just going straight on, and pushed me off into a big lamp post and down a ditch!"
Froome, who also retained the polka dot jersey, was happy to see Thomas make it to the finish, but at the same time sad to see team-mate Pete Kennaugh exit the race due to a respiratory illness.
"I did hear on the radio that (Thomas) had been caught in a crash behind. At that point I was just trying to say to the guys around me 'listen there's been a crash let's just try and keep the race steady for now.' But obviously only a few kilometres before the finish the guys wanted to go hard.
"It's really unfortunate for us to lose Pete Kennaugh at this point. He's a big part of the team but he's had a tough couple of days with illness. I hope he recovers soon. It means we're going to have to share the work between the eight riders but the guys are strong and I've got a lot of confidence in them.” – Chris Froome
With a strong tailwind behind the riders heading out of Bourg-de-Peage at the beginning of the stage, the peloton were pushed along at an average of just under 50km/h early on.
Team Sky again set about controlling the race, but was reduced to eight riders when Kennaugh was forced to abandon the race shortly before the 50km mark.
"Beyond that I think it's been a pretty good day for us,” said Froome. “We saw the other GC teams trying today. Tinkoff-Saxo took the race on at the foot of the last climb. We saw attacks over the top and Vincenzo Nibali going for it.”
Despite attacks on the second-category climb, Froome held firm to retain his lead of 3min 10sec over Nairo Quintana (Movistar) heading into the second rest day.
Vincenzo Nibali (Astana) attacked on the final climb to claw back 28 seconds as the GC contenders finished almost 18 minutes down on the day's breakaway.
Ruben Plaza (Lampre-Merida) timed his attack to perfection on the climb and made good his escape as the rest of the break marked each other. Peter Sagan (Tinkoff-Saxo) took big risks on the descent to claim second place, 30 seconds back.
“I think that's definitely what we can expect these next two days in the Alps,” said Froome, referring to the constant attacks. “The race certainly isn't over yet. We're going to have try and keep control of the race and hope we can keep the lead until Paris."