McIlroy shot a final-round, 1-under-par 69 to finish at 12-under, two shots ahead of Woods and Tom Gillis. With the victory, the Northern Irishman climbed to No. 1 in the world.
McIlroy began the day with a two-shot advantage. He birdied the eighth hole and increased his lead to four shots. After Woods rolled in an eagle putt on the final hole to briefly pull within one, McIlroy rolled in an eight-foot birdie putt at No. 13 to push his lead back to two.
Woods began the day at 2-under. He eagled the third hole and shot 31 on the front nine. Woods birdied No. 17 and then closed with eagle at 18 to close with 62, his lowest final-round score.
"It was just a matter of time before everything fell into place," Woods said. "It just felt good today."
Vaughn Taylor, of Evans, shot 70 to finish tied for 18th place at 2-under. Augusta native Charles Howell recorded a hole-in-one on the seventh hole - a 4-iron shot from 197 yards - and finished with 73 to finish tied for 26th at even-par.