Philipsen, who was led out superbly by his Alpecin-Deceuninck team-mate, world champion Mathieu van der Poel, comfortably held off Eritrea’s Biniam Girmay and Germany’s Pascal Ackermann, who finished second and third.
Slovenia’s Pogacar finished safely in the main bunch, as the threat of crosswinds and echelons failed to materialise on an uneventful 187.3km run from Orleans to Saint-Amand-Montrond.
The UAE-Team Emirates rider leads Remco Evenepoel of Soudal-Quick Step by 33 seconds, with defending champion Jonas Vingegaard of Visma-Lease a Bike in third, one minute 15 seconds further back in the general classification.
Philipsen was the dominant sprinter 12 months ago, claiming victories in four of the first 11 stages at La Grande Boucle.
But until now it had been a largely frustrating Tour for the 26-year-old this year.
A crash on stage three left many riders – including Philipsen – out of position and he was pipped to the line as Mark Cavendish claimed his record 35th stage win two days later in Saint-Vulbas.
A demotion from second to 107th came on stage six after he deviated from his sprinting line – almost colliding with Wout van Aert – and he was unable to match Girmay on stage eight in Colombey-les-Deux-Eglises.
However, with Van der Poel expertly providing assistance, Philipsen finally secured a stage win as he narrowed the gap to Girmay from 96 points to 74 in the race for the green jersey.
“We had some bad luck. I am really happy – it is a big relief. We can finally show our strength, with our lead-out train and did finally what we came for,” he said.
“Mathieu is a really strong guy. When he can show his power and play his part, there aren’t many riders who can emulate him. Having the world champion as your lead-out guy is fantastic.”
On Wednesday, the race crosses the rolling terrain of the Massif Central as it travels 211km from Evaux-les-Bains to Le Lioran.
