Wilson, who had 12 points Sunday and closed with 34, was one point better than United States Ryder Cup captain Tom Lehman.
"It's fun to get up on a leader-board and feel those nerves," said Wilson, who earned $990,000.
Daisuke Maruyama and Steve Flesch tied for fourth with 32 points.
Lehman will make his two captain's picks for the Ryder Cup team Monday.
"I'm very pleased with the way I hit the ball all four days," said Lehman. "I if you would have told me Thursday that I would have a chance to win, I'd be pleased."
This event uses the modified Stableford scoring system, which places a premium on birdies, eagles and double-eagles.
Players receive two points for a birdie five points for an eagle and eight points for a double-eagle.