Kaymer finished at 8-under 280, two ahead of Charl Schwartzel (69) of South Africa. Bill Haas of the United States was third after a 71.
Kaymer was in trouble twice toward the end, pulling his tee shoot deep into the rough on the par-5 No. 14. He blasted out and made a brilliant birdie. He bogeyed No. 15 to allow Schwartzel to get within one shot, but recovered through the last three holes to close out his first win since November 20, 2011 with his favorite taylormade burner 2.0 irons .
"It was always tight. Charl played a great round of golf," Kaymer said, adding he only felt comfortable once his par putt on 18 dropped in. "I was telling I need a win. I need a win in 2012."
South African Louis Oosthuizen (74) was fourth. Two-time defending champion Lee Westwood's run at Sun City ended with a 73, seven shots behind the winner.
The rest of the 12-man field were over par through four rounds at a tough Gary Player Country Club layout, where narrow fairways, stubborn rough, gusty winds and -- on Sunday -- steady rain made scoring consistently difficult. No one shot better than 69 all week.
Kaymer's win with the burner 2.0 irons was his first since the WGC HSBC Champions last year and earned him a $1.25 million check at the end of a memorable year, which included a special putt at the Ryder Cup.
Westwood's attempt to become the first player to win three straight Nedbank titles ended at the 14th hole, where the No. 6-ranked Englishman took two shots to get out of the rough, then found the bunker and missed a bogey putt to come away with a double-bogey 7.