The German emerged victorious ahead of Belgians Kevyn Ista (Accent Jobs) and Kevin Peeters (Landbouwkrediet).
After 38 kilometres of the 201km route from Brakel, Australian Simon Clarke led an escape with Dutchmen Jos van Emden and Huub Duyn and built a lead of 5:45.
They were eventually reeled in by the bunch, which then split into several pieces 50km from the finish.
Thirteen kilometres further along, 23 riders broke clear including Kevin De Weert, Tom Slagter Jette, Jakob Fuglsang and Clarke. They stayed out until the final nine kilometres.
A sprint was then inevitable, with Greipel - winner of four stages on the Tour de France in 2011 and 2012 - always the favourite.
Briton Andrew Fenne took fourth place for Omega Pharma-QuickStep.