Johnson, the 2007 Masters champion, used a late charge to finish at 16-under-par 268 for a two-stroke victory over fellow American Nick Watney, who shot 64 on the rain-softened course in the penultimate event of the FedExCup play-offs.
Lifted by clutch birdie putts at the 16th and 17th holes, Johnson moved to fourth from 27th on the points list going into next week's Tour Championship in Atlanta, where the overall winner of the four-event series pockets a $10 million bonus.
The top five in the standings among the 30 players on the points list that qualified for the season-ending event are assured of winning the FedExCup with a victory at East Lake.
Tiger Woods, Henrik Stenson of Sweden and Australian Adam Scott top the standings with Matt Kuchar holding the fifth spot.
It was the 10th career US PGA title for Johnson, who has yet to win in back-to-back weeks during his 10 years on the tour.
"Frankly, I'm going to have to forget about this week," he said about his approach to winning the Tour Championship.
"I'm going to have to take Atlanta for Atlanta and just play. East Lake is not Conway Farms. It is a beast. It's a classic and a challenge that myself and all my peers get juiced up for."
Johnson made three birdies on the outward nine and then pulled away with a slick downhill 20-foot birdie putt from just off the green at the 16th and followed it with a 13-foot birdie on the next hole to build a two-shot advantage.
Watney was already in the clubhouse after his brilliant round that moved him to 12th on the points list after beginning the tournament outside the Tour Championship field in 34th place in the FedEx standings.
Jim Furyk, who surged into early command of the tournament with a second-round 59, led by two shots after a birdie at the 10th took him to 15 under par, but three late bogeys in gusting winds dropped him to a level-par 71 for third place at 13-under 271.
For Furyk it was the sixth time since his last victory at the 2010 Tour Championship to clinch the FedExCup title that he has failed to win after holding the 54-hole lead of an event.
"I hit the ball plenty good enough, but I didn't make the putts when I needed to," said Furyk, who began to round with a one-shot lead.
Sharing the lead with playing partner Steve Stricker during the round, Furyk said they both suffered from the same fate.
"I think that was kind of the story of our group. Strick hit some beautiful putts today and lipped a bunch out, and it just seemed like he was all over the hole, and we didn't see a bunch go in today."
Tied for fourth place at 11-under were Americans Steve Stricker (72) and Hunter Mahan (67), Australian Jason Day (66) and Briton Luke Donald (66), who moved from 54th place in the standings into 28th place on the points list to qualify for the Tour Championship.
"It's very surreal to play a PGA event on your home course," said Donald, a member of Conway Farms, who closed with 67-66.
"I needed a big week this week and I needed all the help I could get. But it was nice to come up with the goods the last couple of days."
Dustin Johnson barely hung on to the 30th spot on the list by finishing with a 72 for nine-over 293.
The two players that were inside the top 30 entering the tournament and fell out were Briton Lee Westwood and American Harris English.
Westwood, who came to Conway Farms in 30th place, shot a final-round 74 to finish on 12-over 296 and fell to 41st on the list, while Harris just missed out in 31st after a 72 finish put him at three-over 287 as he fell from 28th place.
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