The Manxman finished ahead of Denis Galimzianov of Russia and Jevgeni Goetarovitsj of Belarus in Schoten (Antwerp).
The Briton raced ahead during the final sprint. Wouter Weylandt and reigning champion Tyler Farrar both fell.
Five riders led the race for most of the day: Belgians Andy Cappelle and Baptiste Planckaert were joined by Boucher, Malori and Isajtsjev. The peloton remained in the vicinity though and closed the gap towards the last 20 km.
Belgium's Tom Boonen, who fell twice, did not take part in the final sprint. Switzerland's Fabian Cancellara and Norway's Thord Hushovd relaxed 7 km from the finish.
Weylandt and Farrar made contact and the Belgian crashed to the ground.