The 27-year-old Englishman finished at 22-under 266, and wound up holding off Rafa Echenique after the Argentine produced an albatross ' a two on a par-5 ' on the 18th hole to complete his 10-under 62.
I have been playing well recently but things have often seemed to be going against me, Dougherty said. I thought my time had come, but then within a minute the news came through from the 18th green and I thought Oh no, not again.
Miguel Angel Jimenez (65), Flipe Aguilar (66), Grame Storm (67) and David Drysdale (69) finished another shot back at 17-under 271.
Dougherty looked as though he would win easily when he made his ninth birdie of the day at the 15th to take a four-shot lead over the rest of the field. But that advantage lasted only a moment, because about half a mile away a large German crowd that had gathered around the 18th green witnessed Echeniques remarkable shot.
Echenique, ranked 157th in Europe this year and struggling to win enough money to keep his tour card, holed a three-iron from 243 yards out for a double-eagle that took him to 21 under and instantly turned the pressure back on Dougherty.
He kept his nerve, making par on each of the last three holes, and tapped in on the final green to add to his previous victories at the Alfred Dunhill Links Championship in 2007 and the Caltex Masters in 2005.
Dougherty began the final round three shots behind Goosen and one back of local hero Bernhard Langer, two players with a combined four major titles during their careers.
Dougherty apparently wasnt impressed. He birdied his first three holes and remained at the top of the leaderboard the rest of the round.
Langer, who will be 52 in August, saw his bid to become the oldest winner on the European Tour fizzle as he settled for a share of ninth place after shooting 72.