Heavy rain wiped out most of the morning and at the close, Californian Brendan Steele led by two strokes over Texan Patrick Reed after shooting birdies on each of his first four holes before darkness fell.
Reed had an impressive 67 to move six-under and has the advantage of not needing to finish his round on Saturday.
Overnight leader Jim Herman, the journeyman American who shot a 65 on Thursday, managed just three holes, making par on all to stand five-under.
England's Luke Donald shot a 67 to move four shots off the lead alongside compatriot Ian Poulter and Ireland's Padraig Harrington, who had not finished their rounds.
McIlroy found it hard going in the Champion Course's notorious winds.
The Northern Irishman, playing in his first PGA Tour event this year, bogeyed his first hole, the par-4 10th, and then made another bogey after finding water on the 18th.
After a birdie on the par-3 fifth hole he closed with three bogeys from the last four holes.
The cut is projected for three over-par and while it may change before the leaders finish their rain-delayed round on Saturday, McIlroy can safely pack his bags for the short journey to his home in Jupiter, Florida.
"I'm pissed off. I don't like missing cuts. You want to be playing on the weekend, and I'm not going to be playing which is not nice," he said.
McIlroy had not missed a cut since the 2014 Irish Open and his last missed cut in the U.S. was at the 2012 U.S. Open.
He has been in outstanding form, finishing in the top two in five of his last six tournaments including victory in Dubai.
"I guess after coming off a three-week break, I felt, I wouldn't say rusty, but just not quite on top of my game yesterday," McIlroy said.
"And then today I felt like I was trying to get something going and couldn't. Coming off three weeks off and playing in conditions like these, it sort of shows you where your game's at. I've just got to regroup and get ready for Miami next week."
He will be assured four rounds in the limited field at the WGC-Cadillac Championship.
(Reporting by Simon Evans, editing by Gene cherry)
Share
