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, who was on such a high last Sunday after clinching a European and US Tour money list double.
“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 knew the second putt was to make the cut.”
After missing that one he failed again on the next.
“I feel like I’m hitting the ball pretty good still and I think these couple of days off might actually do me good,” he said. “It’ll give me a chance to rest.”
Campbell has climbed from 910th in the world four months ago to 339th, and the 64 was his lowest Tour round for six years. The former US Open champion made it four birdies in a row on the 10th and added another for nine under.
That put him one ahead of twice winner Miguel Angel Jimenez, China’s Zhang Lian-wei and Swede Fredrik Andersson Hed.
Padraig Harrington was another to miss the cut, but he drew applause on the last by skipping his second shot from the trees across the lake and back onto grass, from where he saved par.
The Dubliner still had to sign for a 75 and six over aggregate, however.
Welshman Rhys Davies, 119th on the money list and needing to stay there this week to keep his card, was one over par with five to play. The cut was predicted to fall at two over.