It was the third time in four years that Kaymer has won the event. The victory will allow him to move to No. 2 in the world, displacing Tiger Woods, when the rankings are updated Monday.
Kaymer shot a 6-under-par 66 and finished the tournament at 24-under 264. He had one bogey in 72 holes -- that coming in Thursday's first round at No. 3, a hole he birdied each of the next three rounds.
Rory McIlroy shot 3-under 69 in the final round and finished second at 16-under. Retief Goosen had eight birdies in an 8-under 64 to jump into a tie for third. Graeme McDowell, who shot 67 Sunday, ended up tied with Goosen at 14-under 274.
Kaymer, who won in Abu Dhabi in 2008 and 2010, entered Sunday's play with the 5-stroke lead and he had pushed that to an 8-stroke bulge three holes into the final round.
He had birdies at Nos. 2 and 3 and made the turn at 2-under. Four birdies over the final nine, including a closing birdie, gave him his ninth tournament title and fifth since winning at Abu Dhabi last year.