The 27-year-old Mahan had an eagle and a pair of birdies in a late four-hole span to finish at 16-under 268. Mahan, whose first victory came at the 2007 Travelers Championship, closed with consecutive bogey-free 6-under 65s.
He’s the eighth U.S.-born player still in his 20s to win more than one tournament.
Fowler, just 21 and a tour rookie, had a final-round 68 for the second runner-up finish of his young career, both of them in Arizona.
In his second PGA tour event last Oct. 25, Fowler lost in a three-way playoff to Troy Matteson in the Frys.com Open just down the road at the Grayhawk Golf Club.
South Korea’s Y.E. Yang also shot a 65 to finish at 14 under, two off the pace. Last year’s PGA Championship winner, Yang led until his tee shot went in the water at No. 17.
Mathew Goggin, Chris Couch and Charles Howell III tied for fourth at 13 under.
Third-round leader Brandt Snedeker struggled mightily with a 78 to wind up far back at 7 under.
The win was worth $1.08 million.
Although he hasn’t won, Mahan has played well the past two years. He played on the 2008 Ryder Cup team and had six top-10s in 2009, including a runner-up finish at the AT&T National. His earnings the last two years topped $5 million.
“It’s just finding a way to win. I just haven’t been able to do it,” he said. “So obviously it feels great to get off the year on my fifth tournament to win. It gives me a lot of confidence in myself that I’m doing the right things in my game, and it feels great, it really does.”
A total of 0.67 inches of rain fell and wind reached 47 mph overnight at TPC Scottsdale and sprinkles lingered Sunday morning. But the rain subsided by the time the leaders teed off at noon.
The tournament, in its 75th year, was known as the FBR Open but returned to its longtime Phoenix Open name when Waste Management Inc. took over as the title sponsor this year.
The poor weather held the estimated final-round crowd to just under 44,000, well off last year’s 60,000-plus. That brought the week’s total attendance to nearly 426,000, down from 470,000 a year ago at the rowdy event that always draws the biggest crowds on the tour.
Yang, whose PGA Championship victory made him the first Asian-born golfer to win a major, eagled No. 10, then reeled off four consecutive birdies to take the lead at 15 under through 15 holes.
Trouble came, though, at No. 17, where his tee shot bounced into the water. Yang’s 25-foot putt for par was on line but stopped an inch short of the cup, and the bogey left him at 14 under.
Mahan, meanwhile, hit his second shot on the par-5 13th 250 yards within 7 feet and made the eagle putt to reach 14 under.
His 18-foot birdie putt on the par-4 14th moved him ahead of Yang at 15 under.
The clincher came at the notorious 16th, the par 3 surrounded by bleachers filled with noisy, irreverent fans who cheer and boo with equal enthusiasm.
Mahan’s tee shot caught the edge of the green and he made the subsequent 14½-foot putt to regain the lead at 16 under.
“You still have a tournament to win, you can’t really worry about the people,” he said. “You just kind of have to block it out, but at the same time kind of enjoy it because you don’t have that opportunity to have so many people watching you on one hole.”
At the 15th, the open desert course’s final par 5, Fowler chose to play conservative and lay his shot up rather than go for the green, which is surrounded by water. He said he felt he was a bit too far away from the pin to go for it, considering he was just one shot back and had what he felt were good birdie chances on Nos. 16 and 17.
“I felt that instead of bringing trouble into play ... I took the safe route,” Fowler said.
That left him with a par, and he missed birdie putts of 14½, 17 and 30 feet on the last three holes.
Mahan sent his girlfriend to his car after he found a crack in his driver early in his round.
“Luckily the rules staff ran her out to the car and she got it before the next tee shot,” Mahan said, “because the next hole is a par 5. I really didn’t want to hit a 3-wood off the par 5.”