While New Zealander Michael Campbell continued his recovery from the depths of despair with a 64 to set the halfway pace, the tournament's defending champion suffered his first early exit since the US Open in June.
McIlroy had four birdies in his first 11 holes to climb to one under par in the tricky wind.
But then came four bogeys in the next five and, with his survival in the balance, a closing double bogey six at the 367-yard 10th for a 72 and five over total.
"I just got on a slide and couldn't stop it," said McIlroy.
"Obviously not the week that I wanted. I was only four off the lead and thinking I could make a couple more and be right back in contention. Unfortunately it just went the other way.
"I still love this course. It's just a pity that this year had to end like that.
"I didn't putt well in Singapore last week and sort of got away with it (he came third). This week was the same, so I think a bit of putting practice is required in Dubai."
He plays the European Tour's season's ending DP World Tour Championship there starting next Thursday.
"I think if I was completely fresh I wouldn't have been making the mistakes. Just one of those things - hit it in the wrong spot and misjudged the speed on a couple of putts. That's just the way it goes.
"On the last I saw the projected cut was plus two, so I wanted to try to hole it (for birdie). I hit it a few feet by, then really knew the second putt was to make the cut."
