Geraint Thomas has predicted that Wednesday’s short but spiky 17th stage of the Tour de France will be “massively decisive” in determining the fate of this year’s yellow jersey after surviving a day of chaos during which he was the inadvertent victim of a police pepper spray.

The 32-year-old Welshman retained a lead of 1min 39secs over his Team Sky teammate Chris Froome after finishing in the pack, following a day where the race was halted for 15 minutes after farmers protesting at French labour laws were blasted by TW1000 pepper spray by police, which ended up drifting into the riders’ eyes. The company which makes the spray says its “active ingredient is extracted from the hottest chilli peppers”.

During a hectic stage, Quick-Step rider Philippe Gilbert catapulted down a ravine on a descent – amazingly he climbed back on his bike, although he later pulled out with a broken kneecap – while another crash near the finish robbed British rider Adam Yates of a brilliant stage win as Julian Alaphilippe overtook him on the final descent. Now all eyes turn to Wednesday’s 65km stage from Bagnères-de-Luchon to Saint-Lary-Soulan, with Thomas knowing that it could make or break his chances of winning his first Tour de France. “It’s going to be massively decisive. It’s the first time we’ve ever done a stage like that, there’s a good two hours of climbing which is a lot over such a short period of time.”

He added: “We’ve got to be clever with it. There’s no point in going too hard from the start because you can run out of legs on that last climb, which is possibly the toughest climb of the Tour. It’s a big, big day and for sure there are going to be some splits.”

Thomas reminded Froome, who is going for a fifth Tour victory, that they had to work together or risk the prospect of the Dutch rider Tom Dumoulin, who sits in third place, beating them both. “There’s a lot of climbing to that point, and the race has been super-hard already. We may find ourselves together having to chase or together in front. But as long as me and Froome don’t race against each other, that’s the main thing. If we do, and Dumoulin wins, that would be a disaster.”

Geraint Thomas rinses his eyes after inadvertently being hit by police pepper spray. Photograph: Stephane Mahe/Reuters

Earlier Thomas and Froome were among the riders affected when farmers who rolled hay stacks across the course were sprayed by police.

“My throat, nose and eyes were burning afterwards,” said Froome. “Quite a lot of riders were in a similar situation so I think we were all grateful for the temporary neutralisation. Thankfully the effects didn’t last long but temporarily everything was stinging.”

Afterwards Matt White, the directeur sportif of Mitchelton-Scott, said that the protesting farmers should be hit with strong sanctions. “I’ve never seen a scene like that in my career,” he said. “That was pretty full-on. We had a 30-second warning about a protest coming up and then the protesters went a bit crazy.”

Photographs emerged of women farmers being sprayed in the face at close range by police, but White insisted that the police had to protect the riders.

“I think the police did a great job,” he said. “Their priority was looking after the riders, not mad protesters. Those guys are crazy. Whatever message they were trying to produce, we as a bike community have nothing to do with it. Let’s hope they get punished accordingly.”

Meanwhile International Cycling Union (UCI) president David Lappartient has hit back at Sir Dave Brailsford following his comments on Monday that spitting and booing at riders was a “French thing”.

A clearly frustrated Lappartient told reporters: “First thing, there are not just French fans on the Tour. They come from everywhere, and I don’t think it is healthy to make it about nationalities. And this is happening just as we We are trying to call the fans to be calm, to make sure that the riders - their riders - … and especially Chris Froome, are respected. Brailsford is pouring oil on the fire. It’s not very good.”