After numerous attacks including from Aru and Porte, Froome dropped the other GC rivals, with Nairo Quintana (Movistar) and Aru unable to stay with the three-time Tour de France victor.
A stricken Porte was treated by doctors before being carried into an ambulance and taken to hospital, while Martin picked himself up and finished the stage despite going down for a second time. Organizers said he was conscious and speaking.
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.
Richie Porte climbing the Grand Colombier with the yellow jersey group prior to his crash on Sunday.
Thomas had crashed on another descent much earlier in the stage and quit the Tour with a fractured collarbone.
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.
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.
"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.
Stage honours were decided by a rare sprint finish between general classification contenders, with AG2R La Mondiale's Romain Bardet fourth and Fabio Aru of Astana fifth. Two-time victor Alberto Contador (Trek-Segafredo) cracked on the last climb and dropped out of contention.
Three-times podium finisher Nairo Quintana of Colombia also struggled, losing 1:15 to Froome and his group.