Kaymer kept a bogey off his card as he added a classy 67 to his opening 64 to set the early clubhouse target at 13 under, and that proved enough to earn him the halfway lead after Thomas Pieters bogeyed his final hole.
But it was McIlroy who provided the highlight of the second round when he celebrated his first ace in professional competition ??? a perfectly-struck nine-iron finding the bottom of the cup at the 177-yard 15th that lifted him to within three of the lead.
The world No 1 struggled on the greens for much of the day, but he rolled in a clutch par putt from 12 feet at the 17th and holed from similar range at the last for a closing birdie ??? his fifth of the round ??? to cap a six-under 66.
McIlroy had started his day with a pair of birdies just as Kaymer was putting the finishing touches to his second round, and the US Open champion headed off to lunch having extended his overnight lead to five shots.
Kaymer, who has won three of the previous nine events in Abu Dhabi, started at the 10th and soon got into his stride with birdies at 12 and 13 before another at the 18th completed a back-nine 33.
He birdied the first for the second straight day, but a cold putter then halted his momentum until he got one to drop at the eighth before closing with a cast-iron par, and he was delighted with his performance despite letting a few opportunities slip.
“I guess the greens, I can read them very well and my stroke always feels well??when I come here,” Kaymer told Sports 4. “Again, today, I didn’t miss many fairways, which gives you the opportunity to go for a lot of flags.
“To be honest I really believe the golf course plays two or three shots tougher in the morning than in the afternoon, because once you miss the fairway, you’re in that thick, wet grass and then it’s almost impossible to get home in two on the par fours.
“So therefore, I was very happy to shoot five under today.”
McIlroy was denied a place in Saturday???s final pairing by Pieters, who carded an excellent 67 despite not making a birdie at any of the four par-fives.
The young Belgian matched Kaymer???s back-nine 33 and three birdies over the next six holes pulled him level with the leader until his blotted his card at the ninth to close on 12 under.
England???s James Morrison earned himself a place alongside McIlroy in the third round after he birdied the final two holes to complete a six-birdie 67 that elevated him to nine under par.
Morrison shares fourth place with Peter Uihlein, who kept a bogey off his card in a solid 68, while Frenchman Alexander Levy (70) and Australian veteran Richard Green (68) are a short further adrift.
Further down the field, star American attraction Rickie Fowler scraped into the weekend with nothing to spare on two under after labouring to a 75 which was blighted by an ugly triple-bogey eight at the long eighth.
Justin Rose also made the cut on the number after managing four birdies in a workmanlike 69, but his Ryder Cup team-mate Henrik Stenson was unable to avoid a weekend off.
The world No 2 made a gallant attempt to bounce back from Thursday???s torrid 76, but his five-birdie 68 merely lifted him back to level par for the tournament, while defending champion Pablo Larrazabal???s 72 was one too many to make the weekend.