Europe's Ryder Cup star made three birdies and a bogey to move to 5 under on an overcast and breezy day that ensured low scores were again out of reach at Gary Player Country Club.
Louis Oosthuizen (69) is second at 4 under, while fellow South African Charl Schwartzel (70) is two back from Kaymer.
Oosthuizen and Schwartzel are lined up for a final-day push for a first home win at Sun City since Trevor Immelman in 2007. Oosthuizen's round is only the fourth sub-70 score in three days of tough golf in South Africa.
Two-time defending champion Lee Westwood made a late move for an unprecedented third straight Nedbank title by shooting a 70 to sit three off the lead. Bill Haas of the United States stayed in contention with a 71 for a share of fourth with Westwood at 2 under.
With the narrow fairways and unforgiving rough already testing the 12-man field, muggy conditions made driving off the tee even more difficult.
The former top-ranked Kaymer holed the putt that retained the Ryder Cup at Medinah but he hasn't won anything else this year. He is in pole position for something else to celebrate in 2012 after a good par save on No. 12. Back-to-back birdies on Nos. 13 and 14 helped him to a three-round total of 211.
"You cannot play too aggressive at certain holes," Kaymer said of his plan for Sunday, "and even if it is only a level-par round, it is still a good score. If you hit fairways here you have chances and that is my goal."
Kaymer's position means a German double at Sun City is possible this week after Bernhard Langer won the seniors event earlier Saturday.
"Golf is just a matter of sticking to your plan," Kaymer said of his subdued year away from the Ryder Cup. "I have another 20 years ahead of me. Maybe another 30 if you see Bernhard."
Oosthuizen had five birdies and two dropped shots. Schwartzel made three birdies and one bogey.
"All in all, the golf course is getting the better of everyone," Oosthuizen said.
Gary Player's course snagged overnight leader Paul Lawrie, with the Scot bogeying four of his first eight holes to battle to a 75 and slip down to sixth at 1 under. Francesco Molinari made a 78 to be equal eighth.
Westwood, the best player of the Sun City layout during the last two years, found some momentum with three birdies on his back nine but he also made back-to-back bogeys at Nos. 12 and 13 to slow his progress and leave him with a three-shot deficit to make up for a third straight triumph to make Sun City history.
Peter Hanson's 73 left him seventh on 2 over. Justin Rose had a 69 — after a 79 on Friday — to move to a tie for eighth alongside Carl Pettersson (74) and Molinari at 5 over.
An eagle on No. 9 made little difference for Nicholas Colsaerts, the Belgian shooting a 74 for 11th. South Africa's Garth Mulroy is last on 7 over after a 75.