Porte's crash was the most dramatic as he clipped the grass verge on the inside of a bend on the lightning quick descent down the fearsome Mont du Chat, less than 25km from the finish.
It's a bitter disappointment for Thomas, who was hoping to help lead teammate Chris Froome to what everyone hopes is a fourth Tour de France title.
Froome's other rivals followed the Italian, seemingly in order to remonstrate with him and tell him to wait.
BMC sports director Fabio Baldpate said Porte had remained conscious throughout. At the time I was too busy looking for my team vehicle to get a spare bike.
"I just had a bit of a wobble on a switchback", he said.
Bardet is now third at 51 seconds with Uran, who took the winner's 10-second bonus, fourth at 55 seconds.
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Regardless, the fall obviously ended his race, and he was taken to the hospital to get checked out.
Barguil, with Fuglsang the last survivor of the day's break, initially appeared to have been awarded the win until the photo finish made clear that Uran had just pipped him to the line.
Overall, Froome leads Aru by 18 seconds and Romain Bardet by 51 as two-times victor Alberto Contador of Spain cracked on the last climb and dropped out of contention.
After picking himself up, Martin finished in a group including Movistar's Nairo Quintana and Orica-Scott's Simon Yates, one minute and 15 seconds behind the leaders.
"Where I crashed, I don't think it was [too dangerous]".