Spaniard Ruben Plaza (Lampre-Merida) won the 201km route from Bourg-de-Peage, leaving Peter Sagan (Tinkoff-Saxo) second for a fifth time in the race and 16th time in all.
Plaza held off Sagan on a daring final descent of the Col de Manse, where Team Sky’s Thomas was nudged off a precipice by Frenchman Warren Barguil (Giant-Alpecin).
The 29-year-old from Cardiff flipped over his handlebars and tumbled off the road, hitting the telegraph pole.
Amazingly, he recovered to finish 38 seconds behind the group of main contenders as Team Sky colleague Chris Froome maintained his lead of three minutes ten seconds over his nearest challenger, Nairo Quintana.
Thomas, who preserved his sixth place overall, 5mins 32secs behind Froome, said: “We were coming hard right and I was just following the wheel, and then, all of a sudden, Barguil was just going straight on and pushed me straight off into a big lamp-post and down a ditch.
“I feel all right for now. The doctor asked me a few questions, my name and stuff. I said ‘I’m Chris Froome’.”
Referring to the abuse Team Sky encountered earlier in the Tour, Thomas added: “A nice Frenchman – they are nice here sometimes, they’re not all bad – pulled me out.
“I lost my glasses as well – they don’t even make those any more.”
Barguil apologised for the incident, while Team Sky principal Sir Dave Brailsford described it as “a big relief” that Thomas emerged unscathed.
The Commonwealth Games road race champion, who had a bike change after the crash, added: “Everyone knows it’s a dodgy descent. I just got taken out. 100 per cent it was a mistake.
“Just stay where you are. There’s only eight or ten of us in a group.”
Froome, who rolled in 18 minutes 12 seconds behind Plaza, was relieved to hear Thomas was okay, with the Welshman an integral member of the squad which will aim to help the 2013 champion through tomorrow’s first of four stages in the Alps.
The race finishes on Sunday in Paris.
Froome said: “He’s a Welshman, that says it all. G’s a tough lad, he’ll bounce back. I’ve got no doubt about it.
“Unfortunately, one rider came underneath him at a corner and chopped him up, took him down, but he’ll be all right and I’m pretty sure he’ll be up there in the Alps.”
Yesterday’s stage was likely Sagan’s final chance to claim a fifth Tour stage win and first since 2013, as the Champs-Elysees finale looks set to be a battle of the pure sprinters.
The Slovakian was among the day’s main protagonists and embarked on a daring descent, but Plaza won by 30 seconds.
Froome, who saw key lieutenant Pete Kennaugh abandon the Tour following illness, allowed defending champion Vincenzo Nibali (Astana) to make gains up the second and final 8.9km climb, but nullified an attack by Alberto Contador (Tinkoff-Saxo).
Nibali gained only 28secs on the Froome group to remain almost eight minutes behind.
Contador stayed fifth, 4:23 behind after his attack was foiled.
“The race is definitely not over, as we could see today,” Froome added.
“All the teams were trying to attack, as we can expect all the way till Paris.
“That’s a small taste of what we can expect these next few days in the Alps, after the rest day. We can expect racing anywhere.
“We’re ready for that. We’re expecting the race is going to come at all different angles.
“Hopefully, we’ve got the team to get the job done.”