Bales of hay blocked the road 26 kilometres (16 miles) into the day's ride from Carcassonne as farmers demonstrated against a cut in state aid. Tour organizers said police used tear gas to disperse the protesters as the peloton approached.
While mountain stages in the Tour are traditionally more than 150 kilometers (100 miles) or longer - sometimes beyond 200 kilometers - this Tour features two legs that are relative sprints by comparison.
After a nine-month investigation - during which Froome constantly protested his innocence - cycling's governing body the UCI, on the advice of experts from the World Anti-Doping Agency, dropped the case just before the Tour began earlier in July. The British cyclist faced a suspension for using twice the allotted amount of a medication that is typically used to treat asthma, according to the Associated Press, but he was allowed to compete.
A gendarme sprays tear gas at protesters as other gendarmes remove haystacks from the route, during a farmers' protest blocking the stage's route.
"Please respect the riders, even if you have a cause to fight for", said Tour director Christian Prudhomme.
"Nothing stuck, however, as the GC men safely negotiated the descent to finish together - ensuring another day in the yellow jersey for Geraint Thomas, who remains 1'39" ahead of team-mate Chris Froome.
Team Sky haven't made a statement about either incident at this point.
This year's Tour has already seen the likes of Froome targeted by fans, and Thomas hopes there will be no further problems over the closing stages.
He told his following that: "As always I will come back stronger!"
"I didn't want him to have a bad day like he did but it just gave me confidence knowing someone of Froomey's stature was struggling, and I just knew I would be able to respond to the attacks".
With 2.5 km to go, Roglic attacked for the second time but was quickly shut down by Thomas.
"It was just about defending that lead", said Thomas.