Riders were seen pouring water into their eyes amid chaotic scenes during stage 16 on Tuesday, after police took action against farmers protesting along the route using bales of hay and tractors.
"The police had to use tear gas on the protesting farmers...some of which has gone into the eyes of the riders, so the race has stopped for now", Team Dimension Data, one of the teams racing, tweeted when the race came to an abrupt stop.
It is nothing new for Sky to face hostility in France but the atmosphere has been even darker this year in the wake of Chris Froome's salbutamol case, in which he was cleared of wrongdoing just days before the Tour began.
It gave Thomas the win after he was second on an nearly identical stage of the Criterium du Dauphine in June, en route to overall victory in the race. If you don't want them to come you could have a Tour de France for French teams if you want but if you want worldwide teams to come then treat them with a bit more respect.
Britain's Geraint Thomas, fresh from winning two stages in the Alps, remained in the leader's yellow jersey.
Police purportedly used tear gas or pepper spray to disperse the protesters - accidentally spraying some of the competing cyclists in the process.
And Thomas said: "It's the last mountaintop (finish) that will be most decisive".More news: US, North Korea hold 'productive' talks on war remains
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Although Sky will be hoping to keep powder dry for the crucial third week, Froome said their rivals could try to steal time on the steep, 3km-long climb to the finish in Mende.
The incidents make teams anxious fans are getting out of hand on the most famous climbs of the Tour.
Thomas maintained his advantage of 1 minute, 39 seconds over defending champion Froome.
This Tour has been marred by incidents as race organizers struggle to deal with angry fans protesting against Froome's participation.
"We've seen the finals of them all", added Thomas, whose bid to become the first Welsh champion of the Tour could be tempered by Froome's ambitions for a record-equalling fifth yellow jersey.
"I can only renew my appeals for calm, for common sense, with regards to the riders who make up the Tour de France".
Thomas praised Froome's "mental strength and his never-say-die attitude", two qualities that he will need to show in the coming days if he's to enter Paris triumphant on Sunday.
"I think the organisers had tried to put in a few special precautions to stop those kind of things happening", he said. Froome has said his training plan was designed for him to come good in the last week.