Just four strokes off the lead at the start of a sun-drenched day at Augusta National, the world number two finished a distant 12 shots off the pace after running up ugly sevens at the par-four 11th and par-five 15th.
On both occasions, McIlroy was thwarted by a sudden gust into his face as he was trying to reach the green. He wound up with a triple bogey on 11 and a double on 15 before shooting a seven-over 79.
"It's disappointing, especially after such a good start," the 23-year-old Northern Irishman told reporters after posting a five-over total of 221 on a firm and fast-running Augusta layout.
"I was only a few off the lead going into seventh hole today and then all of a sudden I play seven through 11 in five over par and basically my chances in the tournament are gone.
"So it's very disappointing. I feel like I was playing well and feel like I have been playing well coming in here. It's just a frustrating day."
Twice major winner McIlroy had been among the pre-tournament favourites after finishing second at last week's Texas Open and a birdie at the par-four third lifted him to three under, just three off the pace.
He then bogeyed the seventh and ninth to reach the turn in one-over 37 and his round unravelled after he drove into trees at the tricky 11th, played back out on to the fairway and then dumped his wedge approach into water.
"The wind switched on me," McIlroy said of his third shot there. "It comes up short in the water and I take seven there. And I never recovered from that.
"Same sort of thing happened on 15. I felt like I hit a good second shot in, the wind gusts back into me, it pitches on the green, but it comes back in the water.
"The margins are very small on this course and when you get on the wrong side of some of these slopes, you can't help but get a penalty. A couple of missed shots here and there and I was done in on 11 and 15."
Especially frustrating for the fast-maturing McIlroy was the fact he had adopted a policy of restraint off the tees this week with the intention of playing into the "fat parts" of the fairway.
"I don't know what I'm going to do," the mop-haired Northern Irishman said. "I feel like I played smart enough. I hit three-wood off the first, five-wood off the second.
"I'm playing it the way I know the way you should play it. I'm not taking too much on, I'm not being too defensive.
"I feel like my strategy's right, it's just sometimes if your execution is just that little bit off you pay a big price for it."
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