Stenson's final round at rainy TPC Boston gave him a tournament record-tying 22-under 262, good for a two-shot margin over Steve Stricker.
The Swede secured his first win four years after coming close twice earlier this season -- he finished second at the British Open and the WGC-Bridgestone Invitational in consecutive starts.
With his third career win, Stenson also bypassed Tiger Woods for the lead in the FedExCup standings.
Woods finished tied for 65th place at 4-under 280.
Stricker (67) secured sole possession of second at 20-under 264, followed by Graham DeLaet (69) at 18-under.