Scott shot a final-round 72 and finished at 18-under-par 270.
Retief Goosen had 70 for 273.
The 24-year-old Scott won his fifth tournament on the European Tour's international schedule. It was his ninth title overall as a pro.
"It was a tough day," Scott said. "Retief played very solid. He kept making pars and putting the pressure on me. I hung in there and I'm very happy with this result."