Katusha said Kittel’s teammate, Rick Zabel, will be allowed to continue in the Tour after race organisers showed clemency since he missed the cut by only three seconds.
Thomas surged to the front around the final bend to win from an elite front group ahead of Tom Dumoulin (Team Sunweb), Romain Bardet (Ag2r-La Mondiale), Chris Froome (Team Sky) and Mikel Landa (Movistar).
Dumoulin is third overall, 1:50 behind, while Nibali recovered to hold on to fourth, 2:37 back, before withdrawing.
“I firmly condemn these incidents”, added Prudhomme, who insisted that most of cycling fans were non-violent.
With Italian Vincenzo Nibali in hospital with a suspected fracture in his back, and Colombian Nairo Quintana now 4:13 off the pace, Sky are in pole position.
More recently, Team Sky rider Richie Porte claimed he was punched by a fan during a mountain stage in 2015 and later had words with a fan who yelled “Doper!” at him as he was riding back to the team bus at the end of the stage.
A couple of minutes earlier, another fan appeared to spit at Froome – confirming pre-race fears that he would run the gauntlet after being cleared two weeks ago of taking excess asthma medication salbutamol.
There were also unconfirmed reports that Froome was spat at by spectators.
Team Sky took control on the final climb of Stage 11 using the likes of non pure climbers Michal Kwiatkowski to do all the work, allowing Egan Bernal to rest for another day.
Now the onus is on Geraint Thomas and Team Sky to defend the yellow jersey as we enter the second half of the race.
“As long as they don’t affect the race that’s the main thing”.
Froome passed long-time leader Steven Kruijswik with 3.5km of the 175km stage to go.
Kruijswijk’s bid was ultimately futile, and he said: “It’s painful”.
“I think I timed my effort perfectly, I’m improving”.
“It’s a big disappointment for me, but I’ll keep on fighting”.
The 2014 champion believed he may have touched a motorbike but television footage suggests he came into contact with a spectator on the right side of a narrow road that lacked barriers to protect the riders. If you take “G” out of the picture, it’s only a slender lead for Froome over his rivals.
Thomas said: “Honestly I’m speechless”.
But the second of three days in the French Alps proved a step too far for the Isle of Man sprinter, who has amassed an impressive 30 stage wins in 10 previous editions. But tragically in the final 400 metres a rampant Thomas stormed past his former teammate for a brilliant win.