The German, whose last victory came at the WGC-HSBC Champions event in Shanghai in November 2011, hit a final round 69 to finish on eight-under-par, two better than local favourite Charl Schwartzel who also shot a 69.
American Bill Haas was a further three strokes back after a one-under 71, one shot better than South African Louis Oosthuizen who was too inconsistent and struggled to a two-over-par 74 and fourth place.
Defending champion Lee Westwood was aiming to become the first player to win the event three times in a row but the Briton's poor putting let him down and he fell away, shooting a one-over 73 to finish fifth.
Kaymer, the 2010 U.S. PGA champion, started well and eagled the par-five second but then double-bogeyed the third to give his rivals hope in the soaking conditions.
Schwartzel emerged as his closest challenger and the former U.S. Masters champion got it to four-under after a birdie at the 14th to trail by one.
But the pivotal moment for Kaymer also came at the 14th. The German badly hooked his tee shot into some dense rough but a superb recovery helped him to get down in two more for a birdie four.
A bogey at the 17th effectively ended Schwartzel's hopes and Kaymer coasted home with three pars over the closing three holes.
World number 32 Kaymer, whose victory gave him the $1.25 million first prize in the 12-man invitational event, told reporters: "The biggest stroke of luck was definitely on 14. I could very easily have made a six or a seven.
"I'm just very happy to finally win this year. I've practised very hard and played very well but it just hasn't happened for me. I said to my caddie, we have to win one tournament every year and this was our last chance."
Kaymer had an eight-week spell as world number one early last year.
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- Charl Schwartzel