The Northern Irishman was in the midst of a two-way tussle with Rasmus Hojgaard for the season-ending event when his Race to Dubai crown was confirmed, with both players locked on 13 under with five holes remaining.
McIlroy valiantly saved par at the 15th hole before hitting his approach inside a foot at the next to card his first birdie in 11 holes and nudge ahead of his rival.
Hojgaard holed a clutch par putt at the 17th to remain one behind but when he failed to find the cup with a birdie effort at the last, McIlroy had two attempts for victory.
He only needed one putt to seal the two-shot success at Jumeirah Golf Estates and complete the end-of-season double.
Australia's Adam Scott finished with a share of third place, alongside Shane Lowry and Antoine Rozner after firing a four-under-par 68. The trio were four shots adrift of McIlroy
McIlroy was pleased to "get over the line" after winning the World Tour Championship, telling Sky Sports: "It means a lot. I've been through a lot this year professionally and personally.
"It feels like a fitting end to 2024. I've persevered this year a lot, had close calls, wasn't able to get it done. So to be able to get over the line...I hung on and got the job done."
McIlroy only needed a top-11 finish on Sunday to reach the summit of the season rankings, with South African Thriston Lawrence, who finished in midfield, the only player able to deny him with a win in Dubai.
Australia's Adam Scott finished with a flourish to be joint third at the DP World Tour Championship. (AP PHOTO)
Lawrence's challenge, however, never materialised and when he came home in one under par for the event, McIlroy secured his third successive Race to Dubai crown with five holes left in his final round.
The world No.3 joins Spanish great Seve Ballesteros in second place in the all-time list with six order of merit triumphs, with only Colin Montgomerie ahead of the pair with eight victories.
After securing his sixth Race to Dubai title, McIlroy said he was proud to be mentioned alongside Ballesteros, adding: "It's really cool. I think everyone knows what Seve means to European golf, to Ryder Cup players.
"He means so much to European golf and for me to be mentioned in the same breath I am very proud."
McIlroy said he was relishing the challenge of attempting to emulate Montgomerie's Race to Dubai titles haul.
He said: "I'm up for it. I've just won my third in a row.
"I've made it my priority to give myself the best chance coming in to the end of the year to win the Race to Dubai and I don't see that being any different for the foreseeable future.
"I will go for my seventh next year and try to chase Monty down."
Another Australian, Min Woo Lee, carded a 70 to finish down the order with a three-under 285.
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