Just two days after Van der Poel held off four chasers after a 40km solo break to win the E3 Saxo Classic race, the Dutchman and his old rival Van Aert came up just one kilometre short of another stunning escape.
Having gone clear with 36km to ride, the pair were caught 4km from the finish by a counter-attack from Belgian Alec Segaert before the peloton swallowed them up with 1,000m to race.
Van der Poel's Alpecin-Premier Tech teammate Philipsen had the strongest kick for the line, with Dane Tobias Lund Andresen in second and Van Aert's Visma-Lease a Bike partner Christophe Laporte taking third.
"This race has been one I've been wanting to win for many years but never had the legs in the end," said Philipsen, who secured a 60th career victory.
"Everything came together today, and I was able to take the victory."
It was agonisingly close for Van der Poel and Van Aert - two one-day classics specialists and long-time rivals - after 240km of a race known as Gent-Wevelgem until it was renamed this year as In Flanders Fields-From Middelkerke to Wevelgem.
"We were both also keeping something for the sprint as well," said Van der Poel, who admitted he had not fully recovered from Friday's efforts.
"If we had gone all out, not thinking about it, we could have made it to the finish. Without Jasper in the back, it would have been a different story," added the 2023 world champion, who has dominated the cobbled classics in recent years but has never won this race.
Van Aert, the 2021 winner, lit up the race with around 57km to ride on the tough, cobbled Kemmelberg climb, bursting out of the peloton and taking Van der Poel and Florian Vermeersch with him.
The trio caught the earlier breakaway riders and formed a lead group of nine, which built a lead of more than 40 seconds on the peloton.
The next time they tackled the Kemmelberg with 36km left, Van der Poel put in a searing acceleration, with only Van Aert able to follow and Vermeersch shipping 10 seconds by the summit, with the peloton cresting a minute back.
It was then a simple pursuit to the finish, with Vermeersch stuck in no-man's land, until he was swallowed up by the group with 12km to go.
The fast-finishing peloton closed to within 10 seconds of the leading duo with about six kilometres to go.
Segaert counter-attacked out of the peloton and even caught the pair with 4km left.
He then kicked for home on his own as the trio were finally caught with a kilometre to race but it was to be the sprinters' day.