The Jumbo-Visma rider pipped last year’s winner Julian Alaphilippe of France on the line after the 305km race through north-western Italy.
It is the second win for Van Aert in a week having claimed the first major one-day race, the Strade Bianchi, in Tuscany.
Australian Michael Matthews of Team Sunweb finished third, two seconds behind the leading pair just ahead of Slovak Peter Sagan, of Bora-Hansgrohe in fourth.
Download our app and read this and other great stories on the move. Available for Android and iOS.