The title holder frittered away stroke after stroke at the European Tour's flagship event and his five-over total of 149 meant he missed the cut by a considerable margin.
McIlroy is in the middle of an untypically busy schedule of five tournaments in a row that will end with the Irish Open at Royal County Down next week.
The 26-year-old Northern Irishman cruised to a seven-shot win at the Wells Fargo Championship in North Carolina on Sunday but earlier this week he complained of feeling "a little fatigued mentally".
McIlroy seemed out of sorts from the start on Friday as he found five bunkers in the first six holes.
On the second the four-times major winner mouthed "did you see that?" at a television camera, as if to complain about the uneven greens, when his putt hit a bump and stopped well short of the hole.
He perked up by bagging his opening birdie of the day at the short eighth, arrowing a pinpoint five-wood within a few feet of the cup.
McIlroy then dropped another stroke at the short 10th before snap-hooking his drive left at the 11th and slumping to a double-bogey six.
More bogeys followed at the 13th and 16th. He almost chipped in for an eagle at the 17th but the three putts he took from 20 feet at the last capped a miserable day.
(Editing by Toby Davis)
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