The world number one's presence at the spiritual home of golf had looked extremely doubtful after he suffered the injury in a kickabout with friends and posted a picture of himself wearing a protective plastic boot and his withdrawal was duly confirmed on his Instagram account.
"After much consideration I have decided not to play in the Open Championship at St. Andrews," the Northern Irishman wrote.
"I'm taking a long-term view of this injury and, although rehab is progressing well, I want to come back to tournament play when I feel 100 percent healthy and 100 percent competitive."
McIlroy's potential showdown with double major winner Jordan Spieth was expected to be the highlight of the Open but the American will now start the tournament as the favourite.
Spieth is one of several players who have come to McIlroy's defence after the usual social media "storm" questioning the wisdom of him playing football on an astroturf pitch so close to the Open.
Spieth said this week that he happily plays basketball with his caddie and also revealed a near miss on a fishing trip after he won the US Open last month when a shark took a tuna he was trying to reel in and almost pulled him overboard.
Phil Mickelson, speaking ahead of the Scottish Open which begins on Thursday, said he missed the 1994 Masters after breaking his leg in a skiing accident.
"I said then, and I feel the same way now, you can't live your life in fear," said the American. "You have to enjoy the moment. I didn't feel like he (McIlroy) was doing anything that was an unnecessary risk. He was just playing around and accidents happen.
"People get hurt taking a shower and doing normal day-to-day things. You can't stop living your life."
Justin Rose took a similar view, suggesting that total focus on golf could be counter-productive.
"It's a tough question, before a major championship...it's probably the last time he does play football in the middle of season," said Rose, who is back at Gullane to defend his Scottish Open title.
"But he likes to have fun. He likes to get his mind away from golf. I think he's the kind of guy that, if he practiced 24/7 and got too much in his own head, it's not going to help him."
(Editing by Ken Ferris and Toby Davis)
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