Clarke, who is chasing a wild card spot on the European Ryder Cup team, finished at 16-under 264. McGinley shot a 64.
Clarke, who also won the Asian Open in April for his first title in five years, heads into the next week's Johnnie Walker Championship in Scotland with a solid chance of earning one of captain Nick Faldo's two wild cards.
"I had two weeks to try to impress Nick," Clarke said. "The first is out of the way and I seem to have done that."
Clarke bogeyed the par-5 second hole, but then made three birdies on the next four to open up a lead against Henrik Stenson. The Swede had birdied the opening three holes, but dropped three shots between the seventh and ninth. Stenson finished in third place, another shot back.
Lee Slattery (65) and Marc Warren (68) tied for fourth at 9 under.
McGinley resigned as Faldo's assistant captain in the hopes of qualifying as a player, but looks likely to need a top performance at Gleneagles to earn a spot.
"There are only two picks, so it's a tight situation, but I'm going to have to win [in Scotland] to give myself a chance," McGinley said. "As everybody knows, it's about winning. I have no complaints -- I have not played well enough, but there's one more event and I'll certainly be giving it 101 percent."