Golf's top two players met for a one-off match on Monday after competing in Shanghai and Kuala Lumpar over the weekend.
Woods defeated the Irish star by six strokes at the World Golf final in Turkey three weeks ago but it was McIlroy who triumphed in Asia with a score of 67.
McIlroy started strongly with two early birdies before Woods responded by chipping in at the 12th hole.
A tense showdown was decided when Woods bogeyed at the 14th, handing McIlroy an advantage he comfortably maintained.
The 23-year-old jets off to Bulgaria later this week to watch his girlfriend Caroline Wozniacki compete in the Qatar Airways tennis tournament before playing in the Singapore Open next week.