Philipsen was also third in Saturday's Omloop Het Nieuwsblad one-day race making the Alpecin man the form sprinter coming into the European season.
The two races that make up "opening weekend" both feature narrow roads, cobbled sections and hills and mark the start of the one-day classics in Belgium, northern France, the Netherlands and Italy.
Philipsen's edged Dutch sprinter Olav Kooij of Visma and the Frenchman Hugo Hofstetter of Israel PT for his first win of the 2025 season.
He won the Tour de France green jersey in 2023 and last year won Milan-San Remo, an ultra-long one-day 'Monument'.
Visma, who won last year with Wout van Aert from a breakaway, tried to set up Kooij over the final kilometre of the 197km run. Philipsen, led out by Kaden Groves, flew past at the finish.