McIlroy held a two-shot lead following an opening 65 and was still one in front when he drove into a fairway bunker on the par-five 18th on the Earth Course at Jumeirah Golf Estates.
After laying up into the fairway, McIlroy then compounded the error by firing at the pin and pulling his approach into the creek which runs the length of the hole.
The resulting double-bogey seven meant McIlroy had to settle for a second round of 70 and halfway total of nine under par, a shot behind Ryder Cup team-mate Shane Lowry, Sam Horsfield and John Catlin.
McIlroy told Sky Sports: “I hit that tee shot (on 18) really well. I actually didn’t expect it to go as far as it did and get up into the face of the bunker.
“And then the third shot, I hit a really good shot. That part of the fairway where the ball was, was quite just sort of thatchy and came up spinny into the wind.
“I hit a good golf shot and felt like I didn’t deserve to be in the water and it was a tricky up and down from there. It wasn’t the greatest way to finish and I was just sort of holding it together most of the day.
“It would have been nice to finish off a bit better but (I’m) still right in the golf tournament. I still feel like I played well and I feel like 70 is sort of the worst I could have shot today, especially with the finish and hopefully that’s the bad one out of the way.”
Lowry and Catlin both shot 65, the lowest score of the day, with Lowry chipping in for an eagle on the 14th and also carding five birdies in a bogey-free round.
“Yeah, that was one of my better ones,” Lowry said of his sublime shot on the par-five 14th. “That was top drawer. That was as good a chip as I hit in a while.
“I knew when I missed it over there it was going to be difficult and I would have been happy to get it within 10 feet, but it came out lovely and hit the flag and went in, which was a Brucey bonus.”
Lowry finished fourth in the Alfred Dunhill Links Championship immediately after making his Ryder Cup debut in September, but has since finished 54th in a 78-man field in Las Vegas and missed his last two cuts.
“I’ve struggled the last few weeks,” the former Open champion admitted. “In hindsight I should have taken a few weeks off and just come here and tried to perform as best I can.
“I spoke to Westy (Lee Westwood) last week, I spoke to Tyrrell (Hatton) and he said after France he really struggled for a few months. It’s something that I wasn’t aware of.
“Since I won the Open at Portrush I’ve spent the next two years trying to make the Ryder Cup team and I’ve reached that, I felt like I left it all at Whistling Straits and then I came back out and I’m just running on fumes.
“Thankfully I’m near the top of the leaderboard this weekend and it will give me something to go out and fight for.”
Open champion Collin Morikawa strengthened his grip on the Race to Dubai title with a second consecutive 68 to reach eight under par, two shots off the lead.
Morikawa would be the first American to win the money list title but said: “I’ve got to focus on the weekend. I want to win this tournament. That’s all I care about.
“Winning this tournament is everything and all else will kind of settle itself.”
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