Hay bales were thrown across the road 29km into the 218km stage from Carcassonne to Bagneres-de-Luchon.
TV pictures showed a policeman using a spray on protesters which then blew into the peloton, with riders pulling over to douse their eyes with water.
There was a delay of about 15 minutes.
There was a short neutralised section before racing began again properly at the 33km mark.
Briton Geraint Thomas, who is in the leader's yellow jersey, and world champion Peter Sagan of Slovakia were among those to be affected.
Several riders went to the doctor's car at the back of the peloton for treatment.



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