10 July, 2017
He beat France's Warren Barguil (Team Sunweb) after a photo finish.
Thomas began the day second in the general classification, 12 seconds behind his Team Sky team-mate Chris Froome, and his exit will come as a major blow for the three-times Tour victor.
His team Racing BMC say he has been taken to hospital.
He won stage one of this year's race and wore the leader's yellow jersey until Froome took it after stage five.
BMC sports director Fabio Baldpate said Porte had remained conscious throughout.More news: Shadow of Mordor free this weekend
Thomas took a tumble on a damp descent of the Col de la Biche, the Welshman's fourth crash on this year's Tour and a repeat of his Giro d'Italia, in which his title hopes ended in a crash with a police motorbike.
On descent of Mont du Chat, the final hors categorie, Porte crashed and skidded across the road and into the side of the mountain wall, with Daniel Martin (Quickstep) unable to avoid crashing into him.
Three riders from the day's break - Movistar's Jesus Herrada plus Alexey Lutsenko and Bakhtiyar Kozhatayev of Astana - had crashed on the same corner as Thomas minutes before the peloton arrived.
Five riders in total crashed out of the race on Sunday while two-time former victor Alberto Contador was able to carry on quickly after coming down on an uphill section.
"I want to thank the other riders, who did not attack", he added, saying he did not see Aru attacking past him as he raised his arms to ask for assistance.
There was also drama on the climb of the Mont du Chat when Froome took exception to Aru making a move when the defending champion had to stop for a mechanical before the Brit's rivals sportingly slowed down.