NORTON, 7 Sept 2015, (AFP) - Fowler overturned a three-shot deficit with eight holes to play at TPC Boston to pip Stenson, carding a three-under-par 68 to finish on 15 under, one shot clear of the Swede.
Fowler's round contained an eagle, three birdies and two bogeys, but it was an error-free performance on the back nine which enhanced the 26-year-old Californian's growing reputation as a nerveless finisher.
Stenson meanwhile was left ruing a double-bogey on the 16th which ultimately cost him victory.
The Swede, who had started the day one shot clear of Fowler, carded a one-under-par 70 to finish on 14 under.
"I really just hung in there today, put myself in a position, hit some good shots made a couple of good putts to keep myself in it," Fowler said.
"Henrik made a couple of mistakes, but it's pretty special to fight it out the way I did."
Three shots behind Stenson on 11 under was Charley Hoffman, who carded a four-under-par 67, one ahead of a clutch of five players -- Jim Furyk, Patrick Reed, Hunter Mahan, Sean O'Hair and Matt Jones -- tied for fourth on eight under.
Earlier, Fowler got off to a dream start, picking up two shots swiftly with a superb eagle on the par-five second with a monster 33-foot putt.
Yet his scintillating start was undone by consecutive bogeys on the third and fourth, before a birdie on the seventh put him back to one under for the day.
Stenson meanwhile had kept his nose in front on the front nine, opening with back-to-back birdies on the first two holes.
A bogey on the fourth was cancelled out by a further birdie on the fifth to leave Stenson two shots clear of Fowler at the turn.
A further birdie at the 10th, with the Swede draining a 14-foot birdie putt left Stenson three clear.
But momentum looked to have shifted on the par-three 11th when Stenson bogeyed and then watched as Fowler sank a 13-foot putt for birdie, suddenly putting the American back to within one shot.
Yet Stenson hit back on the next hole, the par-four 12th, with his fifth birdie of the day, sinking a 36-footer to restore his two-shot cushion with six to play.
Both men made comfortable pars on the 13th but Fowler then produced jaw-dropping 38-foot birdie putt on the 14th to halve Stenson's lead.
Further pars on 15 left the difference at one shot but drama unfolded on the par-three 16th when Stenson's decision to opt for a seven iron off the tee proved costly after Fowler had struck a six iron to within 23 feet.
Stenson's club selection left him short of the green and his ball bounced back into the water hazard forcing him to take a drop.
Fowler duly two-putted for par, and when Stenson missed a 12-foot putt for a bogey four, the American was suddenly in the lead for the first time, up by one shot heading to the 17th.
Pars on the penultimate hole left Fowler ahead as they arrived at the 18th.
Tension mounted as both men missed the green with their approaches. Stenson recovered but then missed a long birdie putt, leaving Fowler to two-putt from 10 feet to win.
Leading final scores from the $8.25 million Deutsche Bank Championship on Monday (USA unless stated):
269 - Rickie Fowler 67-67-67-68
270 - Henrik Stenson (SWE) 67-68-65-70
273 - Charley Hoffman 67-63-76-67
276 - Jim Furyk 71-65-70-70, Patrick Reed 72-67-67-70, Hunter Mahan 69-73-64-70, Sean O'Hair 68-67-67-74, Matt Jones (AUS) 67-67-68-74
277 - Daniel Summerhays 71-68-70-68, Matt Kuchar 69-72-65-71, Jerry Kelly 71-66-68-72
278 - Jason Day (AUS) 68-68-73-69, Brian Harman 70-70-71-67, Harris English 67-74-68-69, William McGirt 73-70-66-69, Gary Woodland 68-70-69-71, Kevin Kisner 71-71-66-70, Louis Oosthuizen (RSA) 73-67-67-71, Kevin Chappell 67-67-71-73, Daniel Berger 68-69-68-73, Russell Knox (SCO) 70-65-68-75
279 - Rory Sabbatini (RSA) 69-74-66-70, Zach Johnson 69-65-74-71, Brendon de Jonge (ZIM) 65-68-73-73