He sealed his first title in nearly a year despite carding a modest 3-under-par 69 in the final round, courtesy of a strong start with three birdies in the first four holes.
Australian Cameron Smith is in a tie for 15th after a one-over-par 73 in the third round to be eight under overall.
Perez, who had been two shots off the lead following a first round 66, hit eight birdies after starting his round on the 10th tee.
Compatriots Rod Pampling and Scott Hend are four over for the tournament.
The Japanese was on fire from the fourth, birdying five consecutive holes before finishing with a run of three birdies from the 16th.
In sweltering conditions, Perez, who led since Friday's second round, birdied three of the first four holes on Sunday to maintain his four-shot overnight lead.
Keegan Bradley (136 total) of the U.S. and Spaniard Rafa Bello Cabrera (137 total) were sixth and seventh respectively.
Defending champion Justin Thomas' chances appear over after he finished the day tied 24th at 6 under, despite posting his best round with a 69.
The US$7-million CIMB Classic is co-sanctioned by the PGA and Asian Tours. "Every year we come it seems more and more people show up, so it's a very cool place". It's kind of similar to this but obviously not as bad as this. I always play well in the heat for some reason, I honestly can't tell you why. "That's all I'm doing", he quipped. "It worked so I'll keep that one".
"So if I can get another six (birdies) tomorrow, I might be tough to catch". "I'm not going to change anything". "This is a big event but there is no cut so I'm only feeling 50 per cent pressure".
Thomas, the PGA Championship title-holder and 2017 PGA Tour Player of the Year, had been in terrific form coming into the event, but failed to lift his game in his mission for a "three-peat".