The Belgian, who rides for Alpecin-Fenix and took the opening stage in a sprint on Sunday, was again fastest to the line as the 182-kilometre stage ended in a chaotic bunch finish at Al Marjan Island, in the emirate of Ras al-Khaimah.
Philipsen edged 20-year-old Dutch rookie Olav Kooij of Jumbo-Visma and Irishman Sam Bennett, who rides for Bora.
"It was a really fast finish," said Philipsen after crossing the line.
"My lead-out man's chain came off in the last kilometre, so it was chaos trying to find a good wheel. It all came out well in the end though."
Pogacar, who rides for the home team UAE, collected a two-second bonus during the stage to double his lead over Italian Filippo Ganna of Ineos.
"I saw the opportunity to take some seconds in the intermediate sprint and took it," said the Slovenian.
"I had a puncture today but I didn't panic, it happens sometimes," he said. "The team was perfect and I was not stressed."
On Friday, the sixth and penultimate stage is again likely to end in a sprint after a 180-kilometre ride round Dubai.
"We'll go for it tomorrow, anything after this is an extra bonus," said Philipsen, who leads in the green jersey classification by 30 points.
The tour ends with a summit finish on Jebel Hafeet on Saturday.
