Bakelants took overall lead from Marcel Kittel after the 96-mile stage that ended in Ajaccio, Corsica.
He crossed the finish line 1 second ahead of a large contingent of riders fronted by Peter Sagan and Michal Kwiatkowski.
Davide Cimolai took fourth and Edvald Boasson Hagen rounded out the Top 5.
Kittel, who avoided a chaotic scene caused by a bus parked at the finish line in Saturday's first stage, ended 17 seconds behind Bakelants in Sunday's competition.
Interpol investigating stolen passports on missing flight
Teacher apologizes for showing sexual image of herself in class