McIlroy had four birdies in his first 11 holes to move to one under par, but that was as good as it got for the Northern Irishman.
Then came four bogeys in the next five and, with his survival in the balance, a closing double bogey six at the 367-yard 10th, where he four-putting the green, gave him a 72 and five over total.
He said: "I just got on a slide and couldn't stop it. I was four off the lead and thinking I could make a couple more and be right back in contention. Unfortunately it just went the other way."
New Zealander Michael Campbell shot a 64 to set the halfway pace.
l European Ryder Cup star
Luke Donald led the way after the second round of the Dunlop Phoenix event in Japan. He was four strokes clear of the field with a 129 aggregate.