ABU DHABI, 16 Jan, 2015 (AFP) - McIlroy had started yesterday's play poorly only to rally late on and Friday was a similar story for the Irishman.
Playing in the afternoon he birdied his first two holes, but a bogey on the sixth meant he made the turn at just one-under par. That is seven shots behind Kaymer, who set the clubhouse mark early at 13-under par.
But the world number one then picked up two shots on the first two holes of his back nine.
Then came his first career hole-in-one as a professional with a perfectly struck nine-iron tee shot on the 177-yard par-3 15th hole.
Another birdie on the final hole meant he finished on six-under par 66, and that sets up an intriguing battle with Kaymer, who is a three-time champion here.
McIlroy has three second places in Abu Dhabi to show, while 22-year-old Belgian Thomas Pieters (67) is sandwiched between the two at 12-under par 132
The cut was applied at two-under par 142, and prominent among those who will miss the weekend action are world number two Henrik Stenson and defending champion Pablo Larrazabal.
Stenson followed up his shocking opening-round 76 with a solid four-under par 68, while Larrazabal (72) dropped three shots on his back nine Friday to miss the cut by one shot at 143.
World number six Justin Rose improved with a 69, while world number 10 Rickie Fowler of the United States just could not recover from a triple-bogey eight on the par-5 eighth and was tied alongside Rose at two-under par 142.
McIlroy, who spent some time after his opening round practicing the driver, was delighted with how he played his second.
"I felt really good. I went to the range yesterday and worked a little bit on a couple of things, and I drove the ball much better today, which you need to do around here,” said McIlroy.
He claims to have made around 10 aces in non-competitive holes, but this was his first in a tournament.
"It definitely made up for the two previous holes (where he missed short birdie putts). It was a perfect number. It was straight downwind, 177, and I had a nine-iron. The 12th hole was playing sort of similar and I hit nine-iron there and pitched 174, so I knew it was a pretty good number,” McIlroy added.
"As soon as it left, it looked like it had a chance. It took a nice little hop to the right. It's my first one ever in competition as a pro, so obviously beers are on me tonight.”
Kaymer shot a bogey-free round and was pleased with his 67.
"I didn’t miss many fairways, which gives you the opportunity to go for a lot of flags,” said Kaymer, who similarly dominated in his previous Abu Dhabi wins and also in the US Open at Pinehurst last year.
Pieters, who made six birdies and joined Kaymer at the top of the leaderboard, made his only bogey of the day on the par-4 ninth, his final hole after starting from the 10th.
"It was solid day. I started off well, but just struggled a little bit coming in,” said the man who lost to Miguel Angel Jimenez in a play-off at the Spanish Open last year.
"I’m just trying to do all the little things right and hopefully it comes together and with a good score.”
Scores on Friday in the Abu Dhabi Golf Championship at the par-72 Abu Dhabi Golf Club:
131 - Martin Kaymer (GER) 64-67
132 - Thomas Pieters (BEL) 65-67
133 - Rory McIlroy (NIR) 67-66
135 - Peter Uihlein (USA) 67-68, James Morrison (ENG) 68-67
136 - Richard Green (AUS) 68-68, Alexander Levy (FRA) 66-70
137 - Gary Stal (FRA) 68-69, Morten Madsen (DEN) 68-69, Tyrrell Hatton (ENG) 66-71, Bernd Wiesberger (AUT) 72-65
138 - Robert Karlsson (SWE) 67-71, Eddie Pepperell (ENG) 70-68, Soren Hansen (DEN) 69-69, Michaël Lorenzo-Vera (FRA) 69-69
139 - Guan Tianlang (CHN) 70-69, Miguel Ángel Jiménez (ESP) 72-67, Alejandro Cañizares (ESP) 69-70, Nicolas Colsaerts (BEL) 68-71, Renato Paratore (ITA) 70-69, Charl Schwartzel (RSA) 71-68, Oliver Fisher (ENG) 69-70, Matthew Nixon (ENG) 68-71, Niclas Fasth (SWE) 69-70, Kiradech Aphibarnrat (THA) 72-67
140 - Kristoffer Broberg (SWE) 69-71, Jamie Donaldson (WAL) 73-67, Ross Fisher (ENG) 71-69, Simon Khan (ENG) 73-67, Steve Webster (ENG) 73-67, Branden Grace (RSA) 66-74, Dawie Van der Walt (RSA) 70-70, Damien McGrane (IRL) 71-69, Yang Y.E. (KOR) 70-70, Anirban Lahiri (IND) 72-68, Emiliano Grillo (ARG) 70-70, Scott Hend (AUS) 70-70, Marcus Fraser (AUS) 72-68, Grégory Bourdy (FRA) 66-74, Raphaël Jacquelin (FRA) 69-71
141 - Victor Dubuisson (FRA) 69-72, Jordi García Pinto (ESP) 70-71, Anders Hansen (DEN) 68-73, Thorbjorn Olesen (DEN) 72-69, Jeev Milkha Singh (IND) 68-73, Maximilian Kieffer (GER) 70-71, Mikko Ilonen (FIN) 66-75, George Coetzee (RSA) 68-73, Richard Sterne (RSA) 71-70, Andrew Johnston (ENG) 73-68, Anthony Wall (ENG) 70-71, Danny Willett (ENG) 70-71, Paul Lawrie (SCO) 68-73, Craig Lee (SCO) 73-68, David Drysdale (SCO) 70-71
142 - Oliver Farr (WAL) 73-69, Bradley Dredge (WAL) 72-70, Rickie Fowler (USA) 67-75, Alexander Norén (SWE) 67-75, Johan Carlsson (SWE) 70-72, Robert Rock (ENG) 69-73, Oliver Wilson (ENG) 71-71, Richard Bland (ENG) 69-73, Seve Benson (ENG) 69-73, Jason Palmer (ENG) 71-71, Andy Sullivan (ENG) 71-71, Justin Rose (ENG) 73-69, Jbe Kruger (RSA) 74-68, Ernie Els (RSA) 70-72, Darren Fichardt (RSA) 69-73, An Byeong-Hun (KOR) 67-75, Jorge Campillo (ESP) 72-70