He had stormed to sixth place with three holes to play but then dropped five shots in the last three holes to finish down in 42nd spot.
McIlroy was later called back to the Augusta National by officials to explain the incident in the bunker on the final hole.
If he was ruled to have kicked sand after failing to get out first time he faced the embarrassment of disqualification, but it was decided there had been no violation.
"I was definitely surprised by the fuss," said McIlroy after his third round. "After my round I didn't even think about what I did until Fred Ridley (chairman of the tournament committee) rang me to tell me what had happened and what he had seen.
"That was 6.30pm [local time] and then he called again and said, 'Do you want to have a look?'.
"I said, 'No - I'm confident I've done nothing wrong'. Then at 8.30pm he said it was in my best interest to come.
Northern Ireland golfer Rory McIlroy explains his actions in the Masters.
"It's a natural instinct for me to smooth out bunker shots. I didn't kick it. I slept OK and it's in the past now.
"The reason it took so long was that I had left the property and I declined first time. I didn't think I was going to be disqualified - it wasn't a tantrum."
Four hours after the completion of his round a statement revealed he would remain in the tournament.
Fellow Northern Irishman
partnered Tiger Woods on Saturday and carded his second successive round of 73 to end the day on one under overall.
After a round that included four bogeys and three birdies, he said: "I'm disappointed. I hung in there with some putts but I knew I needed a 68 to get back in there.
"It's always intimidating playing with Tiger but I had to make sure I paid attention to my game.
"It was an education. It's always great to learn from these guys. I'm a good score away from a good week here."
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