The world's top two golfers met for a one-off match after competing in Shanghai and Kuala Lumpur over the weekend, with McIlroy recording a five-under-par 67 to the American's 68.
Three weeks after Woods defeated the 23-year-old by six strokes during the World Golf Finals in Turkey, it was McIlroy who always held the edge this time.
He had two early birdies and turned two in front before Woods chipped in at the short 12th, but the 14-major champion bogeyed two holes later and could not get back on terms.
Neither player is staying on in the country for this week's WGC-HSBC Champions at Mission Hills.
McIlroy, flying to Bulgaria to watch tennis girlfriend Caroline Wozniacki, next plays at the Singapore Open next week, while Woods has one event left in 2012 - the World Challenge in California at the end of next month.