Philipsen had attracted ridicule last year for celebrating what he believed to be a stage win when in fact Wout van Aert had already crossed the line on a solo escape.
A Netflix series about the 2022 Tour then nicknamed him 'Jasper the disaster'.
On Monday, the 25-year-old outmuscled the other fast men to take the high-speed bunch finish as the Tour arrived in France after two days in the Spanish Basque Country.
The only time the Alpecin-Deceuninck rider trembled was when race Commissioners reviewed the images to check if he had not deviated from his route when he cut off compatriot Van Aert.
There followed a few anxious minutes where Philipsen scrutinised a small screen in the protocol area before his victory ahead of German Phil Bauhaus and Australian Caleb Ewan was approved.
"It was tense," said Philipsen after his seventh win of the season. "Everyone wanted to put everything into this sprint.
"I knew the right side was the most direct. When you're in the lead, you try to take the shortest path. I'm delighted with how my team and above all how Mathieu (van der Poel) led me out for it."
Van Aert finished fifth after the 193.5km ride from Amorebieta-Etxano to Bayonne in southwest France.
"It's hard to say if his sprint was fair, unfortunately I couldn't finish my sprint," said Jumbo-Visma rider van Aert.
"Luckily I survived. That's the most important thing. Tomorrow there will probably be another chance in a mass sprint."
Mark Cavendish finished sixth to miss a first chance to beat the record for Tour stage victories of 34 which he jointly holds with the Belgian legend Eddy Merckx.
However the Briton will be able to try his luck again on Tuesday during the fourth stage which also promises to arrive in a sprint on the Nogaro racing circuit after a largely flat 182km run from Dax.
English rider Adam Yates of UAE Team Emirates retained the overall lead ahead of his Slovenian teammate Tadej Pogacar, the 2020 and 2021 champion, who stays second and wears the best young rider's white tunic.
"Having two leaders will help us when the real mountains start (stage 5 and 6)," said Yates.
"So once we get to the Pyrenees we'll be putting that into action."
Pogacar added: "It was a crazy finale, especially in the last 15 kilometres.
"I tried to stay safe in the finale, as it was a really fast finish but the rest of the stage was calmer. So far, so good.
"We have two easier days from the GC perspective, as I hope tomorrow’s stage is like today’s, and then we will hit the Pyrenees."
Sunday's winner Victor Lafay, who remained fourth overall, held the sprint points green jersey.
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