Team Sky's Thomas suffered broken collarbone, while Porte broke collarbone and fractured pelvis.
'Mixed feelings' for Froome after Thomas and Porte crash out of Tour de France
Chris Froome extended his lead in the yellow jersey on Sunday but was in no mood to celebrate after an incident-packed stage saw both teammate Geraint Thomas and good friend and rival Richie Porte crash out.
Team Sky's Thomas suffered a broken collarbone after falling midway through the stage from Nantua to Chambery, while Australian Porte broke his collarbone and fractured his pelvis in a high-speed crash on the descent of the Mont du Chat late in the day.
BMC's Porte was travelling at 72.5kmph when he touched the grass on the inside of a corner, slid across the road and hit an embankment, taking out Irishman Dan Martin in the process.
"Definitely mixed feelings," Froome said after the stage. "Of course I'm happy to still be in the jersey but at the same time that was a crazy stage.
"I've just seen the images of Richie's crash and that leaves you with a horrible feeling. I really hope he's alright and can make a speedy recovery.
"Of course my teammate Geraint as well, he crashed out with a broken collarbone so I've definitely got mixed feelings after that stage."
Froome looked strong throughout, overcoming a mechanical on the Mont du Chat to finish with the front six and take third place behind the photo finish that separated Rigoberto Uran from Warren Barguil.
When Froome was struggling with his bike, Astana's Fabio Aru - now up to second overall after Thomas's exit, 18 seconds back - attacked before being reigned in by the other contenders and told to respect the yellow jersey.
"At the bottom of the Mont du Chat I had a bit of a mechanical problem and my gears stopped working," Froome added.
"I think Richie was quite instrumental in slowing the group down and basically saying, 'Guys, this is not the time to be attacking the leader of the race', so thanks to Richie and I really hope he makes a speedy recovery."