The world No 1 was just two behind leader Martin Kaymer at the halfway stage but, as the German crafted a sublime bogey-free 65, McIlroy laboured to a 71 despite excelling from tee to green.
McIlroy missed only two fairways and hit 17 greens in regulation, but he struggled to contain his frustration as a succession of birdie chances failed to find the target.
The Northern Irishman, twice a runner-up in Abu Dhabi, did manage to convert excellent approaches at the sixth and 12th holes, but hopes of a grandstand finish effectively ended with a bogey at 13.
After another chance grazed the lip on the final green, McIlroy???s tap-in for par was his 34th shot with the putter as he closed on 12 under par.
A clearly-deflated McIlroy told Sports 4: “I feel like punching myself. I’m very disappointed, I just didn’t putt well ??? yesterday or today.
“I hit the ball just as well as I did yesterday and gave myself so many chances but I didn’t convert any. I was very wasteful today. It looks like I’m playing for second place tomorrow.
“From tee to green I’ve never felt more comfortable. I’m driving the ball great. It’s just a matter of capitalising on the chances you give yourself and I didn’t do that today.
“I tried to stay as patient as possible but it was very frustrating. I started the ball on line for the most part but struggled with the speed as well, so it’s a combination of that.
“You’re always trying to improve and get better and I’m going to have to do something a bit better on the greens to shoot a good number and finish the tournament off well.
“I am now trying to win the other tournament. Martin’s playing in something a little different than everyone else. I think I’m two behind Thomas Pieters and I will try and catch him. It’s obviously very unrealistic that I’m going to catch Martin.”
In contrast, McIlroy???s Ryder Cup team-mate Victor Dubuisson reflected on a fine day???s work after the Frenchman vaulted up the leaderboard with an eight-under 64 ??? the low round of the day.
Dubuisson had been hampered by a back injury in the latter part of 2014, but he appeared to be swinging freely in Abu Dhabi as he rolled in eight birdie putts and kept a bogey off his card to move to 11 under.
But while he was delighted with his performance, Dubuisson still trails runaway leader Kaymer by nine shots and he knows he needs something special over the final 18 holes.
“It was a good day, I played really well. I holed some good putts compared with the other days. I’m very happy about the score,” Dubuisson said. “But I think I’ll need to shoot 10 under tomorrow to have a chance.”
The world No 19 rose to worldwide prominence with his run to the final of last year???s WGC-Accenture World Match Play, and he also played a starring role in Europe???s Ryder Cup victory at Gleneagles in September.
But Dubuisson is keeping his expectations realistic for the coming year, insisting he has not followed McIlroy???s lead in compiling a list of targets for the season.
“I just want to do better for myself, I don’t feel any more pressure,” the 24-year-old added. “Golf is a sport where you can have two or three bad years and then come back. It’s very difficult to keep the same level every year so I’m just trying to do my best on every round, every event.
“It’s difficult to write, ‘this year my target is to win two majors’ because I haven’t even won one. I haven’t won a PGA Tour event, so first I try to keep consistent in my game, maybe win one or two events.”