Van Aert, riding for Continental team Crelan-Vastgoedservice, completed the six kilometre course in 6-52, beating Martin (Etixx-Quick Step) and Reto Hollenstein (IAM Cycling) to the win.
The 21-year-old was making his first appearance in a UCI road race and now finds himself in the leader's jersey heading into stage 1 from Buggenhout to Knokke-Heist on Thursday.
As well as the World Championships in Zolder, van Aert also won the Belgian national championships and the UCI Cyclocross World Cup in 2016.
Lars van der Haar, who finished second to van Aert in Zolder is also riding the Belgium Tour, representing Giant-Alpecin.
Trek-Segafredo's Boy van Poppel also lines up, having been eliminated from the Giro d'Italia on stage eight for finishing outside the time limit, along with Elia Viviani.
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