ABU DHABI, January 17, 2014 (AFP) - The world number seven finished with consecutive birdies to come home in 31.
A round of five-under par 67, which included a double bogey on the front nine, took his two-day tally to seven-under par 137, and in tied fourth place.
The Northern Ireland star was two shots behind leaders Craig Lee of Scotland and Spaniard Rafael Cabrera-Bello.
Lee added a 67 to his 68 on Thursday, while Cabrera-Bello shot a 68 on Friday.
England's Danny Willett made the biggest move of the day.The 27-year-old carded a brilliant rund of nine-under par 63 to move to third place at eight-under par 136.
The turnaround was incredible as he was five-over par after his first 10 holes on Thursday.
World number three Henrik Stenson could not make a move in the right direction and a round of even par 72 meant he missed his first cut since the Quail Hollow Championship on the PGA Tour in May last year.
The Swede was two-over 146 for the tournament with the cutline falling at 144.
The last time he missed weekend action on the European Tour was at the Alfred Dunhill Championship in October 2012.
World number five Phil Mickelson finally found the birdies on Friday, and a 70 moved the American to one-under par 143.
Sergio Garcia survived a ruling scare in the morning, and then recovered well from his overnight round of 76 to post a 68.
Some viewers had called in after the first round, alleging the Spaniard had tapped a spike mark in his line of putt on the 18th hole, in the same manner as Simon Dyson did last year.
But after review, the European Tour cleared the world number 10 after determining he had already tapped a pitch mark.
McIlroy, who looked a completely different man from the one who finished his second round here last year by missing the cut, said: "It wasn't the fastest of starts.
"I started pretty well, I was one-under through five holes, and it was okay, but made a bad swing on the sixth and made double?bogey there.
"Getting back to even par for the round after nine was important, and then I gave myself a target of four-under on the back nine and was able to go one better than that.
"It was a nice way to finish the day. Asked to compare his emotions from last year, McIlroy added: "I feel a little better.
"Coming off the last green last year, after 36 holes, I was deflated to say the least. The week didn't go as how I imagined it or how I planned.
"But I'm happy with how I'm playing. I'm striking the ball really well. I got a few putts to drop on the back nine, which was nice.
"I feel like if I can keep hitting it the way I have been, I've got a great chance to win this tournament."
A delighted Cabrera-Bello said after his 68: "I am playing well, putting good, and putting the ball in play, hitting the fairways... so, I'm feeling confident.
"I'm happy with the way I'm playing with all of the clubs in the bag. There's nothing that I'm complaining about at the moment."
Lee credited his performance on the greens as the key to his success so far.
"I think Santa has brought me a good putting stroke for Christmas. I don't know what's happening out there but I'm holing a lot of putts and that's definitely the difference."
Complete second-round scores in the $2.7million Abu Dhabi HSBC Golf Championship on Thursday at the par-72 Abu Dhabi Golf Club:
135 - Craig Lee (SCO) 68-67, Rafael Cabrera-Bello (ESP) 67-68
136 - Danny Willett (ENG) 73-63, 137 - Thomas Bjorn (DEN) 70-67, Ricardo Gonzalez (ARG) 71-66, Rory McIlroy (NIR) 70-67
138 - Tommy Fleetwood (ENG) 73-65, George Coetzee (RSA) 68-70, Joost Luiten (NED) 68-70
139 - Pablo Larrazabal (ESP) 69-70, Marcel Siem (GER) 69-70, Matthew Baldwin (ENG) 67-72
140 - Robert Karlsson (SWE) 73-67, Gaganjeet Bhullar (IND) 72-68, Alejandro Canizares (ESP) 71-69, Peter Hanson (SWE) 70-70, Thongchai Jaidee (THA) 70-70, Darren Fichardt (RSA) 70-70, Paul McGinley (IRE) 68-72, Michael Hoey (NIR) 69-71, Tyrell Hatton (ENG) 69-71
141 - Miguel Angel Jimenez (ESP) 73-68, Colin Montgomerie (SCO) 73-68, Otto Hennie (RSA) 70-71, Edoardo Molinari (ITA) 70-71, Alvaro Quiros (ESP) 71-70, Jin Jeong (KOR) 70-71, Tom Lewis (ENG) 71-70, Oliver Fisher (ENG) 69-72, Martin Kaymer (GER) 70-71, Marc Warren (SCO) 68-73, Dawie van der Walt (RSA) 68-73