Knox and Thomas both started their final round four shots behind overnight leader Anirban Lahiri of India.
A quadruple bogey nine at the third brought Lahiri back into the pack and Thomas capitalised, carding an eight-under 64 to finish on 23 under, three clear of Japan's Hideki Matsuyama (66).
Knox was 10 adrift after posting a 74.
Thomas, 23, had led over the first two days of the tournament and started his charge with four birdies in his first five holes on Sunday.
"I got a great start and I really was very pleased with how I felt like I handled myself and how I felt out there," he said.
Lahiri, who was looking for his first PGA Tour win, lodged his tee shot in a tree on the third and eventually finished in a tie for third place, four strokes back.
Scotland's Russell Knox fell out of contention on the final day as American Justin Thomas successfully defended his CIMB Classic title in Malaysia.