Knox had started the final round sitting alongside Thomas in joint-second, four shots behind India’s Anirban Lahiri.
The Scot birdied the fifth to move to 16-under for the tournament before following a bogey at the 10th with a double-bogey 6 at the 13th.
He closed with a 74 to finish on 275, 10 shots behind Thomas as he closed with a superb 64 to make a successful defence of the title in Kuala Lumpur.
Thomas had led by two shots at the halfway stage before recovering from a shaky spell in the middle of his third round by closing with five birdies on Saturday.
That burst kept him in contention and he quickly regained the lead in the final round as Lahiri saw his hopes of landing a first PGA Tour title dashed after he ran up a disastrous quadruple-bogey 9 at the third.
Thomas, having already got off to a flying start at the first, birdied the same hole for a five-shot turnaround and stormed to the turn in 31 before picking up three more shots coming home.
He won by three shots from Japan’s Hideki Matsuyama (66) with Lahiri (72) having to settle for a share of third with American Derek Fathauer (67).
“It feels great,” Thomas told Sky Sports afterwards. “I felt very comfortable out there. I played really good all week apart from a stretch on Saturday where I played really poorly.
“I was talking to Rickie [Fowler] last night and he was saying that he had a finish on a Saturday that won him the golf tournament on the Sunday.
“I feel that was maybe the biggest five holes I’ve ever played in my career. Even more important than what I did here last last because I gave myself a chance.
“If I had been eight or nine shots back, I don’t think I was going to have a chance. It was huge as it really gave me a lot of momentum.”
Knox now heads to China, where he launches the defence of his WGC-HSBC Champions title in Shanghai on Thursday.