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.
Froome is looking to win his fourth consecutive Tour de France.
"This new development is exciting for all of us who are behind in the general standings but have the desire to do something", said Quintana's teammate, Mikel Landa, with the stage starting at 15:15 CET.
Britain's Chris Froome puts drops in his eye after being sprayed by tear gas used to disperse a farmer's protest that disrupted the 16 stage of the Tour de France.
This means Tom Dumoulin moves into second place to split the two Sky riders, Thomas and Froome, on the podium.
Bales of hay blocked the road 30km into the 218km leg from Carcassonne to Bagneres De-Luchon.
This summer Geraint Thomas is leading, which I'm sure you all knew because since the World Cup finished you've had nothing else in your life.
Alaphilippe also won the 10th stage and is wearing the polka-dot jersey of the mountains classification leader.
According to French media, the small group of farmers from the local Ariege department protested against the reduction of European Union funding.
"I crashed and it was all my fault". They must be respected, they take enough risks for their job.
"When you come so close to winning a stage of the Tour it's pretty devastating."
But with only 5 kilometers of descent to go, Yates crashed turning a corner and could only watch as Alaphilippe flew past.
Kangert was reeled in by King of the Mountain leader Julian Alaphilippe in the first climb of the day to Montée de Peyragudes, but held on to reach the top ahead of the Frenchman.
Passing briefly through Spain, the route featured three climbs in the finale _ the Col de Portet-d'Aspet, the Col de Mente and the Col du Portillon _ followed by a downhill finish.