After 170km from Mont de Marsan, Philipsen was the fastest again in the final sprint, although Briton Cavendish almost caught the Alpecin-Deceuninck rider by surprise by launching his effort early.
The Briton, chasing a record-breaking 35th Tour de France individual win, was eventually outpowered by Philipsen and had to settle for what might remain the most frustrating runner-up spot in his career.
The 38-year-old Cavendish, back on the world's greatest race after a one-year hiatus, shares the record of stage wins with Belgian great Eddy Merckx, who took his 34 victories between 1969 and 1975.
Eritrea's Biniam Girmay finished third.
"We can't be proud enough of the team. Without them it would have been impossible to win a third stage already. I'm proud of them. We worked together and that led to success," said Philipsen, who once again benefited from Mathieu van der Poel's perfect lead-out.
"I was always on a good wheel and never had to do a big effort before I had to produce my sprint. If you had told me a week ago, I would have told you that you're crazy. We will just continue to add others."
Cavendish threat
Philipsen, however, is wary of the Cavendish threat as the Manxman seems to be getting closer to the record win he has been seeking for his last Tour before heading into retirement at the end of the season.
"He was really strong and I would also love to see him win, like everybody, and for sure he will keep trying, he's up there in good condition."
Cavendish had won the last time the Tour visited Bordeaux, in 2010.
"I'd imagine a couple of teams might protest. He came from the left to the right but it's not for me to discuss," he told reporters.
"I was in a quite good position, where I wanted in the long, straight finish. I was on the right wheel and I kicked a little early but actually I had done the same in 2010. Then I had to sit down. There was nothing you could do. We'll keep trying again."
Saturday's eighth stage is a 200.7km hilly ride from Libourne to Limoges, which could favour Philipsen's team mate Van der Poel, although the classics specialist has pledged allegiance to the best sprinter of the race this year.
"I hope to have a chance of a stage win in the next few weeks," Van der Poel said. "Limoges is a sprint that suits me well but I think we'll be playing 100% for Jasper's green jersey (for the points classification), so it's better to do the sprint for him there."
In the points classification, Philipsen leads France's Bryan Coquard by a huge 88 points with Cavendish a further 28 points behind.
