Spaniard Rahm fired a closing 67 to finish on -20 and seal a career hat-trick at Jumeirah Golf Estates.
England's Tyrrell Hatton (31) and Sweden's Alex Noren (40) shared second place after carding final rounds of 66 and 67 respectively with McIlroy ending at -16 after a closing 68.
Rahm reeled off three birdies before bogeying the fourth and came back with three more to stay ahead before making par at the 18th.
"I like this course and this course likes me. I hope this is the third of many more," he said.
McIlroy secured the Harry Vardon Trophy for the winner of the Race to Dubai to crown the European tour's number one player.
"It means a lot," said the Northern Irishman, a four-times Major champion who last earned that title in 2015 and was already world number one.
"I was a model of consistency the whole way through the year...just a really consistent season, I kept putting in good performances.
"It would have been nice to get a win in here at the end of the year but Jon put in an incredible tournament and fully deserved it. I'm really proud of my year and excited for 2023."
