The Open Champion entered the final round three shots off the lead at Jumeirah Golf Estates but comfortably ahead of all his rivals for the Race to Dubai title.
That all changed as defending champion Matt Fitzpatrick made a surge up the leaderboard and all of a sudden it was all to play for on the Earth Course.
But Morikawa, who was one under for his round after 11 holes, found another gear and signed for a bogey free 66 that left him at 17 under, three shots clear of Englishman Fitzpatrick, who also carded a 66, and Swede Alexander Björk who signed for a 70.
McIlroy, a two time winner of this event, had led for most of the day but dropped three shots in his final four holes to sign for a 74.
The victory for Morikawa is his fourth European Tour win in just 17 events and makes him the only three time winner on the 2021 Race to Dubai.
"It feels so good," he said. "I would be lying to you if I said I wasn't watching what Matt Fitzpatrick was doing today. Boy, did he put on a run. Props to him, made a lot of birdies early on. But it's 18 holes. All I needed to do was catch a spark.
"It's so special. I came here last time, first time to Dubai, obviously not having played too many European Tour events and I told everyone that I wanted to come out here and win - win the Race to Dubai and win the DP World Tour Championship, and I had it in my control this week. Obviously if I won, I would have sealed the deal, and that's all I focused on really.
"I'm still not number one in the world. I still have a lot to work on in my game. Obviously this week was good. I still thought I wasn't playing amazing but I made do. I was able to make some putts here and there, hit some great chip shots, made up-and-down and made some crucial par saves out here and that's what you need.
"So I still think there's a ton to work on. That's just kind of the nature of how my mind works and how I work, I just want more.
"I know I'm going to enjoy this one a lot, especially since it's at the end of the year, but there's a lot more from me hopefully." European Tour