He closed with a third straight 3-under 69 to finish at 18-under 270 on the Eichenried Golf Club course. Els was in front after the first and second rounds and entered the last day as part of a three-way lead.
Thomas Bjorn of Denmark shot a 69 and finished a stroke back. Alexander Levy of France had a 71 and was another stroke off the pace for his best result.
Els is a two-time winner at both the U.S. Open and British Open. He is the first South African to win the BMW International in the competition's 25th edition.
''I'm a very young 43-year-old. There's not a younger 43-year-old, I promise,'' Els joked.
''I've tried a long time to win this golf tournament. I really had it going and then I made it tough for myself again,'' he added, referring to his bogey on the 11th hole.
Els started tied with Levy and Sweden's Alex Noren, but the Swede had two bogeys and fell out of contention while Els, Levy and Bjorn each made three birdies to stay in front.
Bjorn was tied for the lead with Els before a double bogey on the 14th hole – after a bogey on No. 11 –effectively ended the Dane's chances despite six birdies.
The 22-year-old Levy's hopes of a first title ended with four bogeys over his first nine holes.
Defending champion Danny Willett of England shot a 72. He finished with an eagle for a share of 18th place.