Australian Caleb Ewan took second place and German Phil Bauhaus finished third in the fourth stage, a 182km ride from Dax, with Briton Adam Yates retaining the overall leader's yellow jersey.
After the peloton rode at a snail's pace most of the day, things got hectic in the finale on the Paul Armagnac racing track, near the vineyards that once belonged to 1973 Tour champion Luis Ocana of Spain.
With just over 1.5 kilometres to go, European champion Fabio Jakobsen hit the deck on a right-hand bend, with his Quick Step-Alpha Vinyl teammate Julian Alaphilippe saying the riders were caught by surprise by the turns.
"It’s only skin. Today was really chaos. It’s just a big fight, it’s always unfortunate. Really easy stage, nobody was tired so the fight is heavier. It was really a big mess," Quick Step-Alpha Vinyl sports director Tom Steels told reporters.
Half a dozen riders crashed inside the final kilometre, but nothing could derail Philipsen, who again benefited from a perfect lead-out to become the first sprinter to secure back-to-back victories on the Tour since Dylan Groenewegen in 2018.
Philipsen took the green jersey for the points classification leader from France's Victor Lafay.
"Caleb was just next to me he was close to beating me in the end. It's very special to win twice in a row," said Philipsen, who again stayed in Mathieu van der Poel's slipstream until his final effort.
"It's my first time on a car racing track. It was odd. I hope the guys who crashed are OK."
Ewan improved from third place on Monday, but the Lotto-Dstny rider knows he has "some work to do" to beat Philipsen, who has now won the last four bunch sprints on the Tour after prevailing in Carcassonne and the Champs Elysees last year.
The Tour de France hits the mountains on Wednesday with a 162.5km trek from Pau to Laruns, featuring the punishing Col de Soudet (15.2km at 7.2%) and Col de Marie Blanque (7.7km at 8.6%).
Yates leads Tadej Pogacar, the 2020 and 2021 Tour winner and his UAE Emirates teammate, in the overall standings by six seconds with his twin brother Simon in third place, also six seconds off the pace.
Defending champion Jonas Vingegaard is sixth, 11 seconds further back.