There was little drama for most of Wednesday's 179.8km route, which started in Clermont-Ferrand, but it ended with a fiercely contested finish.
This time Philipsen did not have the help of his regular lead-out man, Alpecin-Deceuninck team-mate Mathieu van der Poel, but it made no difference to the outcome.
The 25-year-old followed Wout van Aert through a crowd of riders with 500m to go, then found Groenewegen's wheel before surging past him.
"I can also win without him [Van der Poel], but of course he makes it more easy," Philipsen added. "I had to find my wheel a little bit, and it is also about finding your space.
"It was hectic so it is dangerous for crashing but I was happy I could find a good wheel of Groenwegen in the end. He opened up early, and I could go over."
Defending champion Vingegaard retained his 17-second lead over two-time winner Tadej Pogacar.
Thursday's 12th stage takes the race 168.8km from Roanne to Belleville en Beaujolais, and features five categorised climbs.
ncG1vNJzZmivp6x7o67CZ5qopV%2BovbC%2B02iaspucnruoe5VvaHFoZ2x%2B