Morikawa carded a closing 66 at Jumeirah Golf Estates to finish 17 under par, three shots clear of defending champion Sheffield’s Matt Fitzpatrick and Sweden’s Alexander Bjork.
McIlroy held a two-shot lead when he birdied the second but eventually slipped to a tie for a sixth with a disappointing 74, the Northern Irishman appearing to rip his shirt open in the recording area behind the 18th green.
McIlroy had suffered a cruel piece of bad luck on the 15th and played his last four holes in three over par, but Morikawa was a deserving champion as he birdied five of his last seven holes to secure the first prize of £2.2million.
“It’s really special,” said the two-time major winner, who only turned professional in June 2019. “It’s an honour to be the first American to win the Race to Dubai and to put my name on there with so many greats.
“Two years ago it wasn’t in my thoughts. It was, yeah, let’s go play around the world, but we didn’t know what the cards were going to be dealt.
“To have this chance and close it out, and not just closing it out with a top 10 or something, but to actually win the DP World Tour Championship, which concluded the Race to Dubai, what a great way to finish.”
Fitzpatrick needed to defend his title and for Morikawa to finish worse than ninth to win the Race to Dubai and that looked possible when the Englishman recorded his seventh birdie of the day on the 15th to take the lead.
Playing five groups behind, Morikawa was in a tie for sixth at the time but as Fitzpatrick stumbled with bogeys on the 16th and 17th, the American birdied the 12th, 14th and 15th to join McIlroy at the top of the leaderboard.
A 321-yard drive on the 15th left McIlroy with just 36 yards to the hole, but the former world number one saw his pitch clatter into the flagstick and rebound into a bunker.
McIlroy was unable to get up and down for par to leave Morikawa out in front for the first time and the world number two quickly pressed home his advantage with birdies on the 17th and 18th to secure the title.
“I’d be lying to you if I said I was not watching what Matt Fitzpatrick was doing and boy did he put up a run,” Morikawa added. “He came out firing and was near the lead but it’s 18 holes and all I needed was to catch a spark.
“When I made the turn I knew I was three back at that point but I was able to make birdie on 12, a very tough hole, and just seeing those couple of good shots, seeing that putt go in, just kind of propelled what was to come.”
A fourth win of the year in the Hero World Challenge in a fortnight’s time would see Morikawa overtake world number one Jon Rahm for one week only, but the 24-year-old is determined to secure a much longer stay at the summit.
“I’m going to set some high goals, I always have,” he added. “I’m going to set the bar as high as I can get and keep going.
“I’m still not number one in the world. 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.”