Kaymer, the 2010 PGA Championship winner who also won last year's European money order, birdied three of his last four holes in totaling 18-under 198 at Abu Dhabi Golf Club.
McIlroy finished birdie-eagle in a 65 for the Northern Irishman to move into second place.
"The great thing is I've made only one bogey so far, and that was the first day," Kaymer said. "I played very consistently. I've made a lot of birdies the last three days. My putting is very good. I didn't play as good as yesterday, I think. I missed a lot of fairways, but I got away with it.
"I'm leading by five now, but everybody knows Rory can shoot 5, 6 under in the first nine holes. It will definitely be a great round (Sunday). Leading by five gives me a cushion, but it will be a good challenge nevertheless."
Kaymer beat McIlroy by two shots in last year's tournament, and the Northern Irishman is aware he faces a challenge on Sunday.
"Kaymer is very, very good on this golf course," McIlroy said. "He's always good when leading from the front as well, so I'm going to have a difficult time to try and catch him.
"But you know, I've played great all week. I didn't hole many putts on Thursday, but it's been great. No matter what happens tomorrow, it's been a successful week. All I'm trying to concentrate on is hitting good shots on the course and making good swings at it. If I can do that, the goal that I set myself at the start of the week has been achieved."
David Lynn of England (67) is at 204, two strokes ahead of current Race to Dubai leader Charl Schwartzel of South Africa (71) and Sweden's Alexander Noren (67).
US Open champion Graeme McDowell's putting let him down in shooting a 71 to slip into a tie for sixth place at 207.
Paul Casey of England nailed a hole-in-one at the 12th, finishing in equal ninth place at 210 after hitting a 67.
"I played a 7-iron. It was a beautiful little draw that landed about eight inches just right of the hole," Casey said in a statement. "It probably skipped forward and jumped back into the hole — it was great to see it go in."
Soren Kjeldsen of Denmark and Ricardo Gonzalez of Argentina have also hit holes-in-one during the tournament.
Four-time major winner Phil Mickelson started brilliantly to be 3 under at the turn, only to make four bogeys on the back nine. He hit a 72 for a share of 39th place at 213.
Lee Westwood, the No. 1 player in the world, shot a 73 to be equal 65th.
The yellow metal has seen a steep upward rise, hitting a six-month peak
Expo City's 'throne of peace' near the UAE pavilion has become a star attraction for people to pose
The event takes place at Khalid Lagoon from December 8-10