The Omega Pharma - Quick-Step man beat Daniele Ratto (Cannondale) and Brett Lancaster (Orica) to the line at the end of a 160.7km stage from Girona to Banyoles.
The Belgian now stands 16 seconds ahead of Alejandro Valverde (Movistar) on GC with Danilo Wyss (BMC Racing) four seconds back in third.
Olivier Kaisen (Lotto-Belisol), Christian Meier (Orica) and Maxime Mederel (Sojuan) were involved in the break of the day but they were not given much room by the peloton with their maximum advantage capped at three minutes.
The second stanza of the WorldTour race concluded with four lumpy circuits in Banyoles and the trio were caught with 20km remaining.
A bunch sprint looked inevitable and 27-year-old Meersman made his move with 200m to go to take his second win in as many days and match his entire total for 2012.