The overnight leader bogeyed the 15th hole to see his advantage at the top of the leaderboard cut to one shot by South Africa’s Charl Schwartzel but held his nerve the rest of the way to prevail by two.
Kaymer finished on eight under par overall, with Schwartzel at six under and American Bill Haas alone in third, three further back.
South Africa’s Louis Oosthuizen began the final round just one stroke behind Kaymer, but a 74 today saw his challenge run out of steam and he ended in fourth place on two under, one stroke ahead of defending two time champion Lee Westwood, who carded a 73.
Scotland’s Paul Lawrie, the leader after the second round, went over par for the second day running as he managed 74 to finish in sixth place overall.
Kaymer famously sank the putt that ensured Europe retained The Ryder Cup earlier this year, and has now added a personal crown to his season’s efforts.
"It was always tight,” Kaymer told reporters. “Charl played a great round of golf and I was telling (my caddie) that I need a win. I need a win in 2012.
“I'm very happy to finally win this year, that was the most important thing for me, because I was practising very hard. I played very well the last few weeks and months, but it just did not happen for me on the golf course.
“I said to Craig, my caddie, we have to win one tournament every year and this is our last chance, fortunately we could bring it home.”
The German’s win was preceded by countryman Bernhard Langer’s victory in the Nedbank Champions Challenge, meaning today became the first time that Gary Player Country Club had produced winners from the same country.
Kaymer added: “Bernhard has been a very, very big help for me. There was a little bit more pressure today, everybody was talking about the German double.
“I am very fortunate that everything worked out the way I was hoping it would and obviously very nice from Bernhard that he congratulated me straight away.”
Rainy conditions on the final day were in keeping with the previous three, meaning yet again that scores were kept in check by the weather.
No-one shot better than 69 all week, and that mark was again achieved by Kaymer today having also managed a three under total over the second round.
The German began in positive fashion, hitting a brilliant eagle on the second - only to see his hard work erased with a double bogey at three.
Birdies at nine, ten and 11 took him clear of the pack again, although Schwartzel’s birdie on the 14th trimmed the lead to one.
Kaymer hacked his way out of the rough to make an unlikely birdie on 14 and take his lead back out to two, but a bogey at the next meant the pressure stayed on.
Schwartzel’s victory bid finally stuttered when he hit his first bogey of the day at the 17th, as Kaymer made par the rest of the way to close out an overdue victory.