The 22-year-old American holed a 6-foot par putt on the par-5 18th for a one-stroke victory over Australian star Adam Scott. Thomas shot a 6-under 66 for a tournament-record 26-under 262 total at Kuala Lumpur Golf and Country Club.
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Thomas, who had a course-record 61 in the second round, seemed to have blown his chances when he hit into the water at 14, but immediately rallied with three consecutive birdies to take the outright lead.
Scott, playing two groups ahead, had an eagle and seven birdies in his closing 63.
Thomas led by a stroke coming to the par-5 final hole, which he had birdied on Saturday, but the required par did not come easily. He drove right of the fairway and his approach found the bunker short of the green. He blasted out to 20 feet, raced his first putt past the hole and holed the comebacker for the breakthrough victory.
"I still can’t believe what happened," Thomas said. "I made that par to clinch the title. "I don’t care how I got it done, it just feels awesome,"
Thomas, a close friend of second-ranked Jordan Spieth, continued the early season trend of players in their early 20s claiming their first PGA Tour victories, after Emiliano Grillo at Silverado and Smylie Kaufman in Las Vegas.
The former Alabama star from Kentucky said he had been struggling with downhill lies, and that’s what caused the double bogey at 14.
"I had a big body of water in front of the green, but I told myself I’ve been controlling the tournament so I should not worry too much," Thomas said. "I knew I had four more holes to try to make some more birdies and was fortunate enough get birdies in three of the last four holes."
Scott had a shot at eagle on the last, but the putt was well off target, and that cost him a chance of forcing a playoff.
"Look, 35-footers breaking 4 feet are not gimmes. I threw everything I could at it today. I’m playing well, and that’s nice, because I haven’t played that well for a while," Scott said.
He was aiming to take his form in Malaysia into next week’s World Golf Championships-HSBC Champions in China.
"It’s motivating for sure. I want to get up there and play and show them that the old dog’s still got something," Scott said.
American Kevin Na and Brendan Steele tied for third at 24-under. Na had a 67, and Steele shot 68.
Na lipped out short putts at 16 and 17. He lost a playoff at Silverado and tied for second in Las Vegas in the previous two events. He also tied for second last year in Malaysia, and has eight seconds and seven thirds on the tour against just one win.
Two-time defending champion Ryan Moore had a 69 to tie for 10th at 17 under.