Johnson rolled in two birdie putts over the closing holes at soggy Conway Farms and closed with a 6-under 65 for a two-shot victory over Nick Watney, giving him one of the top five seeds for the Tour Championship next week and a clear shot at the FedEx Cup and its $10 million prize.
His first win of the year came at the expense of Jim Furyk, who endured another dose of final-round disappointment.
Furyk's victory drought is now at three years, and he has failed to win the last six times he had at least a share of the lead going into the final round. He lost the outright lead with a bogey on the 11th hole and then fell too far behind with two more bogeys in his round of 71. He wound up alone in third.
Watney started the week at No. 34 in the FedEx Cup. He closed with a 64, and his runner-up finish allowed him to join the 30 players who advance to East Lake next week, all of them with at least a mathematical chance at the $10 million bonus.
Luke Donald, a member at Conway Farms, made four straight birdies on the back nine and finishing with a par save from the bunker for a 66 that enabled him to go from No. 64 to just inside the top 30 and a trip to East Lake.
The points will be reset, meaning the top five only have to win the Tour Championship to capture the cup.
Tiger Woods will be the No. 1 seed, though he doesn't go there with much momentum. Woods started the final round in cool, breezy conditions just four shots behind and was never a factor after missing a short par putt on the opening hole. He closed with a 71 and tied for 11th, seven shots behind.
''It was not a very good putting week,'' Woods said, who was coming off a tie for 65th on the TPC Boston. ''It's just one of those weeks where I just didn't have it.''
Henrik Stenson, a winner in Boston and angry enough in Chicago that he snapped off the head of his driver during the final round, will be the No. 2 seed at East Lake, followed by Masters champion Adam Scott, Johnson and Matt Kuchar.
Steve Stricker, who played in the final group with Johnson, was one shot off the lead when he started the back nine bogey-double bogey. He closed with a 72, a round that cost him one of the top five seeds.
Furyk had company in his misery.
Matt Jones of Australia had a chance to get to the Tour Championship – which effectively would have put him in the four majors next year – but his 8-foot birdie putt on the last hole hit the lip. That cost him a spot in the top 30.
Harris English was at No. 28 and might have caught the worst break of them all. In a driving rain Sunday, he lost the grip on his tee shot and pulled it into grass so thick the ball was never found. The horn to stop play sounded a minute later, and English went back out Monday morning to No. 8 to play his third shot on the par 5. He wound up with a double bogey, never found momentum and fell out of the top 30 by two shots.
Lee Westwood also fell out of the Tour Championship with a poor week.
Johnson now has 10 career wins on the PGA Tour, and this one capped off an amazing month. Johnson put his postseason in jeopardy by skipping the opening FedEx Cup playoff event to attend his brother's wedding – though he went over to Conway Farms during the wedding week for a sneak preview. He made a 25-foot birdie putt on the last hole at the TPC Boston to earn a spot on the Presidents Cup team, and then won the BMW Championship to get one of the top seeds.
It was a clean performance on the soft, sloppy turf in the north Chicago suburbs.
Johnson played the final 31 holes without a bogey. He got into the mix with birdie putts on the seventh and eighth, the holes were everyone should try to make up ground. He took a share of the lead with an 8-foot birdie on No. 12.
Furyk had fallen out of the lead on the 13th hole by missing a 5-foot par putt. On the 16th hole – the second-toughest in the final round - Johnson took on the flag and went just long into the first cut. He popped it out with his putter and watched the 18-footer roll true to the hole and drop for birdie. Johnson again went at the pin on the par-3 17th and made a 12-footer for birdie to stretch his lead.
He finished at 16-under 268 and earned $1.44 million, pushing his career earnings to just over $30 million.