KUALA LUMPUR, 1 Nov 2015, (AFP) - Thomas' six-under-par 66 left him at 26-under for the tournament, one stroke better than former Masters winner Scott, who nearly snagged a come-from-behind victory with a superb 63.
Thomas, who led after the second and third rounds, nearly threw it all away down the stretch when he chunked a shot into the water on the 14th hole for a double bogey.
"But I just kept telling myself I controlled the tournament before that shot, so I just need to get back in it," said Thomas, 22, who set a course record 61 in the second round.
"I had four more holes to try to make some more birdies and was fortunate enough to do it."
The American rallied to birdie the next three holes and went on to clinch the win, $1.26 million in prize money, and 500 FedEx Cup points.
The hot, humid conditions at the par-72 Kuala Lumpur Golf and Country Club had yielded a slew of sub-65 rounds throughout the tournament, and nothing less than a scintillating performance would win it on Sunday.
Scott, who failed to win a tournament in the 2015 season, nearly caught Thomas by shooting the round of the day, a bogey-free nine-under 63 that included an eagle on the par-5 third.
But a long eagle putt on 18 that could have tied it went wide.
"I threw everything I could at it today. I'm playing well, and that's nice, because I haven't played that well for awhile," said Scott, 35.
Scott is among many players in the field hoping to take momentum into the World Golf Championships event in Shanghai next week.
"I would love to get into contention there and try and win," he said.
"So this is a step in the right direction."
Americans Brendan Steele and Kevin Na tied for third at 24-under after respective rounds of 68 and 67.
Japan's Hideki Matsuyama finished in sole fifth place, two strokes further back.
Seventy of the 77 golfers who completed the tournament finished under par.
The $7 million tournament is jointly sanctioned by the Asian Tour and PGA Tour.
It is the third event of the PGA Tour’s just-begun 2016 schedule.
The win gives Thomas the early lead in the FedEx Cup race, but with a plenty of golf left to play.
Final scores in the $7 million CIMB Classic at the Kuala Lumpur Golf and Country Club on Sunday:
262 - Justin Thomas (USA) 68-61-67-66
263 - Adam Scott (AUS) 68-66-66-63
264 - Brendan Steele (USA) 67-63-66-68, Kevin Na (USA) 67-66-64-67
266 - Hideki Matsuyama (JPN) 65-66-68-67
267 - James Hahn (USA) 70-65-64-68
269 - Scott Piercy (USA) 62-69-69-69, Brian Harman (USA) 70-63-66-70
270 - Tony Finau (USA) 71-67-66-66
271 - Charles Howell III (USA) 66-72-67-66, Jim Herman (USA) 70-66-68-67, Patrick Reed (USA) 68-68-66-69, Ryan Moore (USA) 67-69-66-69
272 - David Summerhays (USA) 71-66-69-66, Cameron Tringale (USA) 70-68-65-69, David Lingmerth (SWE) 73-65-64-70
273 - Branden Grace (RSA) 67-70-69-67, Stewart Cink (USA) 68-64-70-71, Alex Cejka (GER) 66-71-66-70, Spencer Levin (USA) 67-64-68-74