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.
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