The Belgian, riding for Team Dimension Data, attacked at the top of the Cote de Wigtwizzle, the second of four categorised climbs in the final 22 kilometres of the 194.5km stage from Bradford.
He pulled out a lead of more than 30 seconds on the testing Cote de Ewden Height but would need all of it as the chasing pack came back at him on the final climb of the day out of Midhopestones.
He crested the top with nine seconds in hand and eased clear on the descent to Fox Valley to win, with team-mate Omar Fraile following him home.
Team Sky's Tao Geoghegan-Hart finished in fifth.
Read the original article on Eurosport: Belgium's Serge Pauwels is Tour de Yorkshire winner