French police forces dispersed the demonstration by throwing tear gas before riders arrived, according to Tour de France broadcaster France Televisions.
Four-time champion Chris Froome and current Yellow Jersey holder Geraint Thomas were among the cyclists forced to pull over and pour water in their eyes.
Video footage of the incident appeared to show liquid being blown back into the advancing peloton after being sprayed by an officer from France's national gendarmerie against a protestor.
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The pair were together as they reached the end of the second decent and were 2 minutes and 30 seconds ahead of the peleton, but after winning Stage 16 the day before, Alaphillipe ran out of legs and was dropped by Kangert entering the final 16-km climb.
Chris Froome was among a group of riders whose eyes needed treatment when police intervened with tear gas to disperse farmers protesting funding cuts by disrupting the Tour de France on Tuesday.
Froome remained second in the general classification, 1 minute, 39 seconds behind Sky teammate Thomas.
Police were said to be arresting some protesters after farmers threw hay bales across the road before the peloton's arrival.
PETER DEJONG AP Britain's Geraint Thomas solidified his position in the yellow jersey during the 17th stage
Downhills were tricky and former world champion Philippe Gilbert went spectacularly over a low stone wall in the descent from the Col du Portet d'Aspet.
"I knew the last kilometres of the stage".
French rider Julian Alaphilippe has been the king of the mountains so far and could add to Tuesday's Stage 16 victory.
Their field is the road, the road is open - we can not lock them in a swimming pool or a stadium or in a tennis court. "It's bike racing", the Frenchman said.
Yates was quickly back on his bike, and followed home Bahrain-Merida's Gorka Izagirre to finish third.
The last time a Tour stage was blocked by a demonstration was in 2004.
He was gaining time in the descent when Yates went down.
The drama is set to continue on Wednesday as riders take on the challenging Stage 17 from Bagneres-de-Luchon to Saint-Lary-Soulan Col du Portet.
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