An incredible race that was hotly contested from 140 kilometres out came down to the final kilometre, with Van der Poel and Van Aert going up against one another in the biggest one-day race of this autumn season.
And it was the Dutch sensation Van der Poel who edged it after the pair played cat-and-mouse right up until the final 200m.
Van Aert came around his rival at 50m to go and looked to have the momentum after launching the sprint with 200m to go, but the Alpecin–Fenix rider found one final burst to edge a photo finish.
Both riders were made to wait for confirmation of the result, but the contrast in emotions was stark when Van der Poel's win was confirmed.
The two riders had been part of a three-man lead group along with world champion Julian Alaphilippe, but the Frenchman suffered a horrible crash with 35km of the race remaining.
The Elegant–Quick-Step rider collided with a motorbike and went down hard, bringing his race and his season to a painful conclusion.
Watch the moment Julian Alaphilippe crashed into motorbike at Tour of Flanders
"The motorbikes were slowing a bit, going slower than the riders," Sean Kelly explained.
"Van der Poel was also very close and flicked out and got around them, but Alaphilippe did not see it in time, touched the side of the moto and looks to have done some damage."
The sprint for third place was won by Alexander Kristoff (UAE Team Emirates), edging out Anthony Turgis from Total Direct Energie.
Van der Poel's father Adrie won the Tour of Flanders in 1986, and Mathieu's victory today makes them the first father-son duo to have won the same monument.
It was a crash-filled and chaotic edition of the race, with Gregor Muhlberger taking home the award for the most innocuous chute of the day.
'He'll be embarrassed' - Muhlberger causes his own crash in unfortunate musette accident