Bales of hay blocked the road 30 kilometers (18.6 miles) into the 218-kilometer stage from Carcassonne to Bagneres-de-Luchon.
A gendarme sprays tear gas at protesters as other gendarmes remove haystacks from the route, during a farmers' protest blocking the stage's route.
The Tour de France is the world's biggest and most iconic cycling race.
The race restarted around 15 minutes later.
This means Tom Dumoulin moves into second place to split the two Sky riders, Thomas and Froome, on the podium.
Simon Clarke of Australia cleans his eyes after tear gas was used by policemen against the farmers who protested during the Tour de France cycling race between Carcassonne and Bagneres-de-Luchon, France, July 24, 2018.
The incident occurred when the 36-year-old was descending the Col de Portet-d'Aspet - the hill which claimed the life of Italian rider Fabio Casartelli in 1995.
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"I knew the last kilometres of the stage".
The Quick-Step Floors rider got a slice of luck along the way, overtaking leader Adam Yates after he crashed off his bike in the final descent.
In the end it was British rider Yates who won the climb to Col du Portillon, and looked set to win his first Tour stage.
According to the Associated Press, the hay bales were thrown into the road ahead of the race's lead pack by farmers facing an even more grueling challenge - the reduction of European Union funding. They must be respected, they take enough risks for their job.
"Do not add to danger for the cyclists", Prudhomme said.
"I was not affected because I was not in the first 10 of the group", he said.
Earlier in the stage, Alaphilippe's team mate Gilbert was also in the race lead on the descent of the Portet d'Aspet but fanged it too hot into a corner, crashing over a wall and into a ravine.
Yates was quickly back on his bike, and followed home Bahrain-Merida's Gorka Izagirre to finish third.
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Hussain's family, in a statement to CBC News , denounced his "horrific actions" and said he was suffering from mental problems . The 29-year-old brutally gunned down his victims, who included aspiring nurse Reese Fallon , 18, and a 10-year-old girl.