The cyclocross world champion made his final move on the last uphill drag to the Piazza del Campo in Siena, and Frenchman Alaphilippe, the 2019 winner, was unable to follow.
Colombian Egan Bernal, the 2019 Tour de France champion, took third place after the trio jumped away from a select group of riders following Van der Poel's first brutal attack on the last 'sterrato' - one of the dirt road sections peppering the 184-km course.
"It is one of the races I really wanted to win, I felt really good. I launched an attack in the last gravel section and then I still had something left," said Van der Poel, who completed a Dutch double after Chantal Van Den Broek-Blaak prevailed in the women's race earlier on Saturday.
"I gave everything. It was amazing to finish off this way."
Defending champion Wout Van Aert took fourth place after cracking when his great rival Van der Poel, who beat him at the cyclocross world championships in January, powered away with only Alaphilippe and Bernal.
Van Aert was then the strongest of the chasing group, which also featured Tour de France champion Tadej Pogacar, British hot prospect Tom Pidcock and Austrian Michael Gogl.
