McGowan shot a 1-under-par 71 at the Centro Nacional course, finishing at 25-under 263.
Mikko Ilonen closed with a 66 to take second place, three strokes back at 266.
David Drysdale was third at 267 after shooting a 67.
The 27-year-old McGowan was ahead by seven beginning the round but had his advantage trimmed to two strokes at No. 14. He birdied 15 with a 12-foot putt and parred out for the victory.
"I came here this week in form and it's lovely to come away with the trophy," McGowan said. "It means a lot to win. That's another goal out of the way and hopefully from here I can progress and move on to bigger things."
Gareth Maybin (64), Alexander Noren (65) and Gary Murphy (68) tied for fourth place at 18-under 270.