HAIKOU, October 28, 2013 (AFP) - In the 'Match at Mission Hills', at a sprawling golf complex on Hainan Island, the Northern Irish world number six shot six-under-par 66 to Woods' 67 in the one-round face-off.
McIlroy, who has dropped off the top of the rankings and has not won a tournament all year, also beat Woods by one shot in a similar Chinese event last year.
Monday's victory, at the same venue where he won the World Cup with Graeme McDowell in 2011, will give him a boost ahead of this week's WGC-HSBC Champions in Shanghai.
"I would like to play all my tournaments in China where I can beat Tiger," said the 24-year-old.
"It's been great to come back to this wonderful golf course where I still have such great memories from playing here two years ago in the World Cup."
Last year's 'Duel at Jinsha Lake' was notable for its unruly fans, and marshalls and officials -- and Woods's manager -- again struggled to control the crowd at times on Monday.
Woods, who touched down after a 22-hour journey late on Sunday, was also battling a virus caught from his daughter, with his voice reduced to a whisper by the end of the round.
"I don't sound all that well now but it was nice that it was warm out there today as that certainly helped, because I think my fever broke and I can start feeling a bit better," said the world number one.
"But I tell you what, when you have kids they bring home some strong bugs and this one has definitely been kicking my butt for the last couple of days."
McIlroy got off to a great start when he birdied the first two holes before Woods, competing in his first event since the Presidents Cup, responded with birdies at three and four.
McIlroy shot a double-bogey on the fifth and he trailed Woods by a stroke coming into the par-five 12th, where both players raised a cheer by firing eagles.
The Ulsterman drew level with a birdie at 14 and it was Woods who blinked first when he three-putted for bogey on 17. Both players finished with a birdie on the last hole.
It was an encouraging outing for McIlroy, who finished tied second at the Kolon Korea Open before fading from a promising position at last week's BMW Masters in Shanghai.
"So I leave here and head back to Shanghai with my game good and there has been a lot of promising signs in practice and in my competitive play," he said.
"I still have four tournaments left to the end of the season and still would love to finish 2013 strongly and get some momentum into next season.
"I'm hitting the ball well and from tee-to-green the game is very solid and if I can get the putter working, I maybe can contend and get a win or two."
Woods is remaining in Asia for promotional engagements before heading to Turkey and next week's inaugural Turkish Airlines Open at Balek.
While the appearance fee was not revealed, reports said Woods and McIlroy split $3 million for playing last year's 'Duel'.