McIlroy made two massive birdie putts towards the end of the front nine – a 31-footer on the par-4 eighth, followed by a 16-footer on the ninth – to move to 15-under par and lead by three shots.
At the same time, his playing partner and overnight leader American Cameron Young struggled and made the turn at two-over with two bogeys.
On the back nine, McIlroy made a bogey on the par-5 13th and could not add another birdie, but that was enough for a winning total of 14-under par 274.
The 34-year-old has started the defence of his Race to Dubai Rankings with a runner-up finish and a win as he looks to become Europe's No. 1 for a sixth time, moving to the top of the rankings for the 2024 title and the International Swing.
"It's a great start to the season," he said.
"I started well last year with the win here. A couple of little things still to work on but these weeks are great. You learn a ton from them and obviously great to get the competition and come out on top as well."
Poland's Adrian Meronk once again showed his massive talent, and a last-hole birdie gave him a solo second place at 13-under par.
World No. 25 Young, searching for his first win on elite tours, finished third at 12-under par.
With his fourth title at the Emirates Golf Club, the world No. 2 McIlroy surpassed South Africa's Ernie Els and became the most successful player in the 35-year history of the championship.
Chile's LIV Golf star Joaquin Niemann made the most of his limited starts on the European tour, finishing tied fourth at 10-under alongside Spain's Pablo Larrazabal and Canada's Aaron Cockerill.
