McIlroy claimed the top ranking after it had eluded him last week when he fell to Hunter Mahan in the title round of the WGC-Accenture Match Play Championship.
The 22-year-old reigning U.S. Open champion from Northern Ireland finished at 12-under 268. That was good for a two-shot victory over Woods -- who blazed to a career-low round of 8-under 62 -- and Tom Gillis (69), both of whom finished at 10-under 270.
Woods made a charge with a pair eagles, including one at 18, en route to his best-ever single round. But it wasn't enough as McIlroy responded by draining a 10-foot birdie putt at the 13th hole to move two shots clear for the world's former top-ranked player.
Lee Westwood grabbed sole possession of fourth place at minus-8 with a 7-under 63 Sunday.