Perfectly set up by his Alpecin-Deceuninck teammate Mathieu van der Poel, Philipsen came out on top in a long sprint, beating German Phil Bauhaus (Bahrain Victorious) and Australian Caleb Ewan (Lotto Dstny), who were second and third respectively.
Briton Adam Yates, who won the opening stage on Saturday, retained the overall leader's yellow jersey as the race entered France through the Basque country.
There was some concern that the Tour could be affected following a wave of rioting in France, triggered by the fatal shooting of a teenager by police last week, but no incidents were reported along the road or at the finish.
Monday's ride, despite some short climbs at the beginning of the stage, was meant for the sprint specialists and American Neilson Powless and France's Laurent Pichon, the two breakaway riders of the day, were reined in easily well before the final straight.
Philipsen was a cut above the rest, finishing off his team's work in impressive fashion for his third career win on the Tour and his seventh victory of the season.
"It's not easy to stay on Mathieu's wheel," said Philipsen, who has now won the last three bunch sprints on the Tour after Carcassonne and the Champs Elysees last year.
"Everything went according to plan, he's the perfect lead-out rider. When he goes it's hard to go past him. We've been working hard and I'm really happy it has worked as early in the Tour as today."
Van der Poel, who has not shown great form in the first two stages, was up to the task on Monday.
"It was a quiet stage, until the last 40 kilometres when it got dangerous," said Van der Poel, who has not shown great form in the first two stages.
"I think it was a perfect lead-out from the team and I had to bring him to the 300m line."
Briton Mark Cavendish, who is looking to break the record of 34 stage wins on the Tour he shares with Belgian great Eddy Merckx, was sixth.
Cavendish is riding his last Tour de France.
