Tour organizers said police used tear gas to disperse the protesters as the peloton approached. Jeff Pachoud / AFP/Getty Images Great Britain's Geraint Thomas, right, wearing the leader's yellow jersey, and other riders wait for the race to resume. Froome was treated with eye drops and Sagan poured water over his face to clean his eyes.
Jack Bauer was the first New Zealander to the finishing line in stage 17, in 2 hours, 41 minutes and 38 seconds, 20 minutes behind Quintana.
According to French media, the small group of farmers from the local Ariege department protested against the reduction of European Union funding.
This Tour has been marred by incidents.
Froome was jostled and spat at on Alpe d'Huez, while 2014 victor Vincenzo Nibali saw his race ended after he was brought down in a tangle with a fan on the same mountain.
"Obviously I didn't want him to have a bad day, like he did", Thomas said after watching Froome struggle.
Spectators have been taunting four-time champion Froome since he was cleared of doping just before the race started, while Thomas has been whistled and booed at for being Froome's teammate.
Thomas now leads the Tour by one minute 59 seconds from Team Sunweb's Dumoulin, with Froome two minutes and 31 seconds back.
Thomas held an overnight lead of 1min 39sec on compatriot Froome, but took it to 2:31 after the four-time champion crossed the finish 1:36 behind Quintana and almost a minute off Thomas.
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"It's pure happiness after a day of suffering", said Alaphilippe, who tightened his grip on the polka dot jersey for the mountains classification.
Just as Yates got back on his bike, Alaphilippe sped past, looked around at the Englishman and surged ahead.
"I wanted to win for my people in Colombia, after months of hard work", said Quintana, who has won the Giro d'Italia and the Vuelta.
"Today it was a really insane day".
"He looks really strong so I imagine he'll be able to finish it off", said Froome.
Asked about riding in service of Thomas as the defending champion, he added: "That's professional cycling, that's what a team is all about".