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.
He plays the European Tour's season-ending DP World Tour Championship there starting next Thursday.
Campbell has climbed from 910th in the world four months ago to 339th - he was once 12th - and the 64 was his lowest Tour round for six years. The former US Open champion went to the turn in 30, made it four birdies in a row on the 10th and added another from 10 feet at the last to reach nine under.
That put him one ahead of Miguel Angel Jimenez, Zhang Lian-wei and Fredrik Andersson Hed.