JOHANNESBURG, Dec 2, 2012 (AFP) - The 27-year-old sunk four birdies at the 7,162-metre Gary Player Country Club and came out ahead of Schwartzel despite a double-bogey on the third immediately after his eagle on the par-five second.
"The eagle at the second hole was a bonus -- two great shots and a nice putt. The third obviously wasn't so good as I hit a bad tee shot and got into trouble," said the relieved former world number one.
"But for me the biggest luck today was definitely on 14 with my tee shot, and then making a birdie. I could very easily have made a six or a seven, so that was very lucky that I found that ball in the perfect position and could chip it down the fairway and make four from there," he said.
At one point he was tied with South Africans Schwartzel and Louis Oosthuizen as well as Bill Haas from the United States at five-under, but his consistent play at the rainy northwestern Sun City resort saw him through.
The German's first victory this year crowns a difficult return after a bad season. World number one early in 2011, Kaymer's performance slumped toward the end of the year.
His putt clinching the European victory in the Ryder Cup in September heralded the old form he was used to.
"I'm just very happy to finally win this year. That was the important thing for me, because I've practised very hard and played very well the last few weeks and months but it just hasn't happened for me on the golf course," he said.
"I said to my caddie that we have to win one tournament every year and this was our last chance," he said.
Schwartzel hit the same round of 69 as Kaymer, but though his four birdies closed the gap, a bogey on the 17th saw him end two strokes behind the winner.
Defending champion Lee Westwood from England carded a one-over-par 73 to end with 287 -- seven behind Kaymer. His tepid performance saw him miss the record to be the first player to win the "African Major" three consecutive times.
Kaymer takes hom $1.25 million in prize money.
In what turned out to be a German affair his countryman Bernhard Langer won the senior section of the tournament with a seven-under-par 209 on Saturday, two strokes ahead of runner up Jay Haas, father of American Bill Haas.
Scores after the final round of the Nedbank Golf Challenge invitation tournament at par-72, 7162-metre Gary Player Country Club Sunday:
280 - Martin Kaymer (GER) 72-69-70-69
282 - Charl Schwartzel (RSA) 72-71-70-69
285 - Bill Haas (USA) 70-73-71-71
286 - Louis Oosthuizen (RSA) 71-72-69-74
287 - Lee Westwood (ENG) 71-73-70-73
289 - Paul Lawrie (SCO) 71-69-75-74
290 - Francesco Molinari (ITA) 72-71-78-69, Carl Pettersson (SWE) 72-75-74-69
291 - Peter Hanson (SWE) 72-73-73-73
293 - Nicolas Colsaerts (BEL) 70-78-74-71
295 - Justin Rose (ENG) 73-79-69-74
297 - Garth Mulroy (RSA) 75-73-75-74