Early-morning fog on Friday at Abu Dhabi Golf Club had forced suspension of play that caused the second round to be completed on Saturday.
The start was once again delayed, this time by two hours and 50 minutes.
McIlroy, playing alongside world number one Jordan Spieth and number six Rickie Fowler, came back to complete his remaining five holes, and was still without any birdie and one-over for the round when he stepped on the 17th tee.
“I said, let's finish 3-3 and I was able to that,” said McIlroy, who made a birdie on the par-4 17th and then smashed a laser-guided five-wood second shot that almost holed out for an albatross.
The Northern Irishman tapped in for an eagle to finish on two-under par 70.
“I knew I needed something and I knew I wanted to finish well and I knew 18 was a chance and 17 playing downwind, I would have a wedge in there. So I knew I had a couple of good chances.
“But I didn't quite expect to do it on 18 there. That was a nice way to finish,” said McIlroy, who finished tied for second place alongside first-round leader, American amateur Bryson DeChambeau (72).
“It was an average round to be fair but that's the thing, even when you're not really at your best, to be able to come away with a 70 and still keep within it up of the leaders, I'm really happy with that.”
Spieth (73) parred his last five holes to remain at three-under par, while Fowler (68) started with a bogey on the 14th hole, but added a couple of birdies on the 16th and 18th to be tied 11th at six-under par.
The cut was applied at one-under par 143.
Original source: Late birdies boost Mcllroy