After bogeys on the first two holes, the 25-year-old Englishman birdied No. 6, 7 and 8 on the Old Course at St. Andrews and finished at 18-under 270.
Justin Rose shot 69 for second, while Northern Ireland teenager Rory McIlroy had a 67 for third. Barry Lane (67) and Paul Lawrie (71) shared fourth place at 274.
The 18-year-old McIlroy turned professional after the Walker Cup last month and earned his full Tour card in only two events. He was 42nd in the British Masters last month.
Ernie Els (71) tied for sixth with fellow South African Trevor Immelman. Els had a triple-bogey 7 at the 16th, where he putted from just off the back of the green into a bunker. He took four more to get down, and three-putted with a miss from 2 feet.
Dougherty's other European Tour victory came at the 2005 Singapore Open. On Saturday, Dougherty shot a 6-under 66, his best round at St. Andrews.