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Scott Stallings, who took a five-shot lead into the final round, hit his second shot at the par-five 18th into the water and didn't make the playoff that included Gay, Sweden's David Lingmerth and Charles Howell.
The trio finished 72 holes on 25-under 263. US tour rookie Lingmerth had 10 birdies in his 10-under 62 on the Palmer course, where the final round was played after the first three rounds were played over three courses in the southern California desert.
VIDEO: Humana Challange, Day 4 highlights
"It feels amazing right now," said Gay, who struggled last year to make changes to his game designed to give him a bit more length off the tee. "I'm still in a little bit of shock. It kind of happened so fast there at the end the way things went down.
"Last year was a struggle. I just wanted to come out this year kind of refocused, recharged, and believing in myself."
Gay said he went into the final round knowing he needed to be aggressive.
"I knew Scott was five ahead. It was going to be, even with a great round, a really low round, it would be tough to catch him," Gay said.
Gay had nine birdies in his nine-under 63, and Howell countered two bogeys with 10 birdies in his eight-under 64 on Sunday.
Gay had a birdie chance at the last which would have given him the outright lead, but missed his eight-footer.
When he finished, four players were tied for the lead. He was expecting at least one of them to birdie the par-five finishing hole.
"It was a rollercoaster," Gay said. "I was fortunate for that not to happen and have another chance."
Howell had an 88-foot eagle putt at 18 but three-putted while Lingmerth birdied the last hole of regulation.
All three were in the fairway off the tee at the first playoff hole, the 18th. Gay then found the greenside rough, Howell was on the green and Lingmerth was in the water and couldn't match the pars of the other two.
They headed to the par-four 10th for the second playoff hole. Gay found the fairway and hit his approach to five feet while Howell was in the right rough and from there into a bunker behind the green.
After Howell missed his par attempt, Gay made his birdie putt to claim the fourth US PGA Tour title of his career and his first in four years.
Stallings had five birdies but also three bogeys, his two-under effort giving him a 24-under total of 264. He was tied with James Hahn, who had two eagles in a 62 on another day of ideal scoring conditions.
Even after finding the water at 18, Stallings had an opportunity to join the playoff, but he chipped nine feet past and missed the putt.
"I just hit a bad shot at a bad time," Stallings said.
Leading final-round scores on Sunday in the $5.6 million US PGA Tour Humana Challenge on the Palmer Course, Nicklaus Course and La Quinta Country Club course (USA unless noted, all par-72, x-won at 2nd playoff hole):
263 - x-Brian Gay 67-66-67-63, David Lingmerth (SWE) 68-64-69-62, Charles Howell 67-65-67-64
264 - James Hahn 63-67-72-62, Scott Stallings 66-65-63-70
265 - Nicholas Thompson 69-66-66-64, Ryan Palmer 65-69-66-65
266 - Kevin Chappell 68-69-67-62, Jason Kokrak 63-69-69-65
267 - Richard H. Lee 66-65-70-66, Billy Horschel 67-68-65-67, Kevin Streelman 69-65-66-67, Brian Stuard 71-67-62-67, Charley Hoffman 65-67-67-68, Stewart Cink 66-67-66-68
268 - Robert Streb 67-69-68-64, Matt Kuchar 70-64-69-65, Bryce Molder 66-68-68-66, Ricky Barnes 65-68-69-66, Robert Garrigus 66-67-69-66, Bob Estes 69-69-67-63, John Rollins 70-65-64-69
269 - Matt Jones (AUS) 68-68-69-64, Brandt Snedeker 67-68-67-67, Jimmy Walker 66-70-66-67, Zach Johnson 66-66-70-67
