The Northern Irishman claimed a maiden Rolex Series crown at this event 12 months ago but came into the weekend ten shots back before a stunning third-round 63 put him into the final group on Sunday.
He then turned a two-shot deficit into a four-shot lead with six holes to play before a bogey on the 13th gave the chasing Adrian Meronk and Cameron Young a glimmer of hope.
Pole Meronk cut the lead to one as he signed for a 71 but McIlroy held his nerve down the stretch and carded a 70 for a 14 under par total and a one-shot win.
American Young finished with a 74 to sit at 12 under, two shots clear of Canadian Aaron Cockerill, Spaniard Pablo Larrazábal and Chilean Joaquin Niemann.
The win takes McIlroy past Ernie Els' hat-trick of Desert Classic victories and hands him his third Rolex Series triumph, having won three of the last five blue riband events.
He also becomes just the second player to successfully defend this title after Stephen Gallacher lifted the Dallah Trophy in 2013 and 2014 and makes it six wins in Dubai with his two victories at the DP World Tour Championship.
The 34-year-old has started the defence of his Race to Dubai Rankings in Partnership with Rolex crown with a runner-up finish and a win as he looks to become Europe's Number One 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.
"I thought on Friday night, I thought ten under for the weekend, I would have a really good chance to win. I shot 11 and ended up winning by one.
"I've played the game long enough to sort of know how these things are going to go. Thankfully I played the golf I needed to and it's just incredible to get my fourth win here at the Emirates.
"The pivotal point for me came on the eighth and ninth hole - making two threes there, that sort of set me up to try to control it on the way in.
"I made that one blunder on 13 and made bogey there but felt like I steadied the ship well over the last few holes and it was one of those days where there wasn't a ton of fireworks just because the course was so difficult. I held on as best as I could and thankfully no one around the top of the leaderboard made much of a run."
McIlroy drove the 351-yard par-four second and got down in two to sit one behind overnight leader Young, with Meronk also moving to 13 under with the help of a stunning bunker shot on the par-five third.
Young missed a five-footer as he failed to get up and down from the sand on the fourth to make it a three-way tie but McIlroy would soon lead alone as his rivals faltered.
Young had a stroke of bad luck as his drive at the sixth clipped a person down the side of the fairway and ended up next to a tree, causing him to play out left-handed and drop a shot, while Meronk chipped into the water on the seventh and made a double-bogey.
That left McIlroy one ahead and he put his foot down, holing a huge right-to-lefter from 31 feet at the eighth and a 16-foot putt on the ninth to lead by three at the turn.
The advantage was briefly trimmed as Young got up and down from the sand at the par-five tenth but he missed the green at the next two holes and a pair of missed par putts from inside six feet put McIlroy four ahead.
Meronk had missed a short par putt after finding sand on the ninth but hit back with an up-and-down after another excellent bunker shot on the tenth and a two-putt birdie from the fringe at the 13th.
Back down the par-five, McIlroy was in the trees after going a long way left off the tee and as he made a bogey, Meronk put an approach to four feet at the 14th and cut the lead to one.
It was back to two after Meronk found nasty rough with his first and second on the 16th, a hole where McIlroy made a brilliant par save after sending his drive into the waste area and Young holed a 25-footer to rejoin Meronk in second.
Meronk then made a two-putt gain on the last and while that was not enough for the win, it did give him solo second as Young finished bogey-birdie, with McIlroy parring the last for the title with the minimum of fuss.
Larrazábal carded the lowest round of the day with a 66, two shots fewer than Cockerill and four less than Niemann.
Dane Nicolai Højgaard, Japan's Masahiro Kawamura, China's Li Haotong and Australian Adam Scott finished five shots off the lead.