He lay motionless on the road for some time, being attended to by medics before being taken to hospital, although organisers said he was conscious and speaking.
Champion Chris Froome retained the yellow jersey after finishing the stage third, behind Frenchman Warren Barguil, who missed out on victory in 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.
"I had a mechanical problem with my gears, I had to change bike", Froome said. From what I understand it looked like Richie (Porte) had said to my other rivals, "Listen guys, this is not the moment to attack when the leader of the race has got a mechanical".
GRAPHIC IMAGES: Richie Porte seriously injured after horrific Tour de France crash
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. He is now eighth overall, a massive 2:13 off the pace.
After a well-earned rest day, the Tour resumes on Tuesday with a largely flat 178km Stage 10 from Perigueux to Bergerac, which should reopen the doors to the sprinters.
The accident also saw Irish rider Dan Martin felled as he collided with the prone Porte. Fuglsang completes the top five at 1:37 while Martin will be relieved to have emerged from that frightful collision with Porte just 1:44 in arrears.
Quick-Step Floors rider Martin got back on his bike after he took a new wheel from a neutral support vehicle.
Slovakian Juraj Sagan, Italian Matteo Trentin and Australian Mark Renshaw also finished outside the time limit.
Joey Chestnut wins his 10th Nathan's Famous Hot Dog Eating Contest
Carmen Cincotti finished in second place with 68 hot dogs, while Matt Stonie , the 2015 first-place victor , placed third with 48. In 1916 , Polish immigrant Nathan Handwerker opened a nickel hot dog stand on Coney Island with a $300 loan from two friends.
Intertek Group plc (ITRK) Stock Rating Lowered by Goldman Sachs Group, Inc
After $0.58 actual EPS reported by OneSavings Bank PLC for the previous quarter, Wall Street now forecasts 10.34% EPS growth. The average 12 month target price among brokers that have covered the stock in the past year is GBX 177.86 ($2.26).
India welcomes GST: Historic midnight session of Parliament
Shampoo and washing powder will be charged at a rate of 28%, and will be expensive under GST. So, many taxes, 17 taxes going into one is definitely going to get simple", she said.
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