Lidl-Trek rider Pedersen earned his first victory of this year’s race with a blistering sprint on the home straight.
Pedersen burst past Italy’s Marco Frigo on the final stretch of what was classed as a medium mountain stage to seal victory in four hours, two minutes and 13 seconds.
Frigo, riding for Israel-Premier Tech, the team targeted by the protests, came in third behind Orluis Aular of Venezuela.
Pedersen’s team-mates worked hard for him in the day’s large breakaway to give him his chance to win the stage.
“The boys were working so hard to make it possible,” Pedersen said.
“In the end it makes it even nicer to win when everyone is looking at us, everyone knew our plan, and still we succeed.
“When Frigo went [with] 700 to 800 metres to go it was perfect, because he provided a leadout. I was closing him slowly and at the corner it was time to open the sprint.”
The peloton, featuring Pedersen’s compatriot Vingegaard and the other main contenders, finished 13-and-a-half minutes after the winner crossed the line.
After a rest day on Monday, the race resumes with stage 16 on Tuesday, a 167.9km with another medium mountain stretch from Poio to Castro de Herville.