There was a 27-year gap between his first and final victory at the tournament.
But the 2006 US Open victor fought back with two rounds of 66 to get inside the top 25 then turned on an exhibition over the opening nine holes of the final day.
The Swede reeled off three consecutive birdies from the 15th hole to take the lead before parring the demanding last, sinking his winning putt from inside three feet to edge young American Ollie Schniederjans at Sedgefield Country Club.
On a hot afternoon when spectators resorted to hand fans in an effort to keep cool, Henrik Stenson was red hot when it counted Sunday.
"I don't feel like I have a lot of pressure to perform", Stenson said. "It was a tight race". "I came back strongly, great birdies coming home and right where we want to be".
The win makes him the winningest Swedish player of all-time on the US Tour, surpassing Jesper Parnevik and Carl Pettersson who both have five.
Stenson made four birdies in a five-hole stretch from 13-17 for the second straight day, then sank a 3-foot par putt on 18 to win the Wyndham Championship with a 22-under 258, a record low for the event's 32 editions at Sedgefield Country Club's Donald Ross course. "That was a performance of a lifetime and the scoring that we did showed that".
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Ollie Schniederjans pushed Stenson all the way to the final hole.
His best finish this season was a tie for 14th at the Canadian Open, and he had a string of seven consecutive tournaments from April-June in which he either withdrew or missed the cut. 13-15 " and celebrated by dabbing.
Cristie Kerr and Paula Creamer won key matches, and Gerina Piller sealed it with a birdie putt that put her 3 up over Florentyna Parker with three to play in a 4-and-2 victory.
Ryan Armour, who shared the second-round lead after shooting a 61 on Friday, slumped to a 72 despite an eagle on the fifth hole.
"It was anyone's tournament on the back nine", Stenson said.
Cameron Smith was the best of the Australians closing with a 7-under 63 to claim a share of 7th place, while Geoff Ogilvy's tie for 16th ensured the Victorian's season will continue for at least another week, raising him to 116th on the FedEx Cup points list after beginning the week in the final playoff exempt position of 125th.
The 2013 FedEx Cup champion and 2016 British Open victor was at 16-under 194 at Sedgefield with a round left in the PGA Tour's last regular-season event of the season. But even with that, he should still finish in the top 125 and have his PGA Tour card for 2017-18 as well as earn a spot in the playoffs.