World No. 1 McIlroy rolled in a birdie putt from around 15 feet at No. 18 for a 4-under 68 that left him a stroke clear of Reed, who shot 65.
McIlroy captured the title for the third time and has started a year with a win for the first time in his career.
“It was a battle all day. Honestly it has been a battle all week,” McIlroy said. “I really feel like I haven’t had my best all week, but I managed my game and played really smart.
“I managed my game well, lots of room for improvements. … Mentally, today, it was probably one of the toughest rounds I’ve ever had to play because it would have been really easy to let your emotions get in the way.
“I’m going to enjoy this. This is probably sweeter than it should be or needs to be. … A really good foundation for the year.”
The Northern Irishman started the round with a 3-shot lead — and 4 ahead of Reed — but was overtaken on the back nine by the American, who picked up 7 shots in his first 13 holes.
Reed bogeyed No. 16 but made birdie at No. 18 to put pressure on McIlroy, who finished on 19 under overall.
The pair traded verbal blows Wednesday after an interaction — of sorts — at the practice range Tuesday that saw McIlroy snub Reed, who had gone over to wish the Northern Irishman a happy new year.
Reed walked away before lightly tossing a tee — featuring a logo of his 4 Aces team in the LIV Golf league — in the direction of McIlroy, one of the most vocal critics of the Saudi-run breakaway series.
Reed said it was “unfortunate” that McIlroy didn’t shake his hand and was quoted as describing McIlroy as “an immature little child.”