The Dutchman had too much in his locker at the line for defending champion Kenny Van Hummel, the Vacansoleil-DCM finishing second.
Mark Renshaw made it a good day for Rabobank as he claimed third place, with Andre Greipel of Lotto Belisol in fourth.
"Finishing first and third, you can only be happy," said Nico Verhoeven, Rabobank's directeur sportif. "But I am also happy with the way it happened. Mark led out the sprint for Theo and still finished third himself, behind Kenny van Hummel but ahead of André Greipel.
"This is really considered a sprint race, and if you end up winning with your sprinter and the team did everything according to the book, you obviously go home with a very good feeling."