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.
With his wins at Royal St George's Golf Club, the WGC-Workday Championship at The Concession and in the UAE, the World Number Two becomes just the the second player ever to win a Major Championship, a WGC title, a Rolex Series title and the Race to Dubai after Francesco Molinari, and the first to win them all in the same season.
"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."
McIlroy found himself in a tough spot on the par five second but sent an exquisite pitch high in the air to set up a birdie and open up a two shot lead.
He got up and down from the sand to save par on the third but could not repeat the trick on the fourth and had company at the top from the charging Fitzpatrick.
The 27-year-old put an approach to six feet at the first and got up and down at the second before hitting smart irons into the sixth and seventh and holing from 37 feet on the eighth to turn in 31.
Another beautiful iron shot to ten feet at the tenth put him in a share of the lead and after being very comfortable all week, Morikawa was all of a sudden one shot from losing his place at the top of the Race to Dubai.
An excellent up-and-down brought Morikawa a birdie at the seventh to ease that pressure but Fitzpatrick rolled home from 19 feet at the 15th to take the solo lead.
McIlroy had been battling on the front nine but he put a stunning approach to tap-in range at the tenth and was soon alone at the top as Fitzpatrick did well to drop just one shot after finding water at the 16th.
Another bogey after finding sand off the 17th tee dropped Fitzpatrick two back and he was alongside Morikawa, who holed from 16 feet at the 12th for a birdie.
Fitzpatrick hit back with an up-and-down from the sand on the 18th to set the target at 14 under but a lovely deft chip from Morikawa set up a birdie at the 14th and the Race to Dubai leader was just one behind McIlroy.
He soon had a share of the lead courtesy of a wonderful iron shot to nine feet at the 15th and led on his own after McIlroy hit the pin with his second at the same hole and saw his ball run into a bunker.
McIlroy may have been suffering some bad luck but Morikawa was making his own and he put his tee shot to 20 feet on the 17th and rolled home the putt for a two shot lead before making a two putt birdie on the last to seal an ultimately comfortable victory.
A three putt at the 16th essentially ended McIlroy's chances before he hit a poor tee shot at the last and found water with his second.
Björk put an approach to five feet at the third and while he broke a run of eight pars with a bogey on the 12th, another approach to five feet had him back in red numbers before he made a two putt birdie on the last.
Højgaard made seven birdies and two bogeys in a 67 that ensured he finished the season eighth on the Race to Dubai Rankings in Partnership with Rolex, one place ahead of MacIntyre who finished his season with a 71 containing five birdies, two bogeys and a double.
Poulter signed for a 67, two shots better than Burmester, with Spaniard Adri Arnaus, English duo Paul Casey and Sam Horsfield, American John Catlin, Dane Joachim B. Hansen and Ireland's Shane Lowry at 11 under.