Leader overnight, the German bogeyed the 15th to have his advantage at the top of the leaderboard cut to one stroke by local hero Charl Schwartzel.
But Kaymer, a former Scottish Open winner and the man who sank the putt that ensured Europe retained the Ryder Cup earlier this year, held his nerve.
He finished on eight under par with Schwartzel at six under and American Bill Haas three strokes further back.
Scotland's Ryder Cup hero Paul Lawrie, the leader after the second round, finished on 74 to be sixth overall.
Kaymer said: "It was always tight. Charl played great golf but I knew I need a win.
"I have played very well in the last few weeks and months, but it just did not happen for me on the golf course, so this is great. It's a great way to round off the year."
Kaymer ensured it was a German-double at Sun City.
On Saturday, fellow German Bernhard Langer took the Nedbank Champions Challenge.
ICE HOCKEY: Braehead Clan slipped six points behind fifth-placed Coventry Blaze in the EIHL when they were beaten 5-1 in the Midlands last night.
Clan were level at 1-1 when Jade Galbraith netted after 24 minutes to equalise Gerome Giudice's opener.
However, two goals from Russell Cowley and a double from Greg Leeb settled the issue.
BASKETBALL: Glasgow Rocks were beaten 85-73 at home against Leicester Riders in a BBL Championship game last night.