Van der Poel's triumph came on a track designed by his father Adrie.
Van der Poel ended Belgian Van Aert's chances of victory in a closing sprint to cap a magnificent three days for Dutch cyclists in front of almost 50,000 home fans at Hoogerheide.
Friday's six-rider relays gold went to the Netherlands with 24 hours later Fem van Empel leading home a Dutch 1-2-3 in the women's title race.
Van der Poel was succeeding Britain's Tom Pidcock, who skipped the event to attend a training camp in Spain, preparing for the road-racing season.
The winner of three road classics Van der Poel revelled in the mud, attacking from the first circuit, only allowing compatriot Lars van der Haar a brief spell in command.
The two headline acts Van der Poel and Van Aert had already pulled streets clear at the business end of the 10 laps of the 3.2-kilometre circuit.
In a thrilling closing duel between the pair on this their 11th cyclo-cross meeting this season it was Van der Poel who held the ace card.
He sprinted clear of Van Aert to pull a couple of bike lengths clear.
Van Aert's Belgian compatriot Eli Iserbyt took third, 12 seconds adrift.