The defending champion quit midway through his second round yesterday claiming he was "in a bad place mentally" on a dramatic day in Palm Beach - then later released a statement to say a sore wisdom tooth was the reason for his early exit.
Beginning on the back nine, McIlroy played his opening eight holes of the round in seven over par, then found the water at the 18th - his ninth hole - and immediately quit the tournament.
It was McIlroy's first ever withdrawal from a tournament as a professional, but the third time this year he has failed to reach Saturday - playing with clubs from his new sponsors, Nike - having missed the cut in Abu Dhabi and been knocked out of the Accenture Match Play Championship in the first round by Shane Lowry.
Fellow Northern Irishman McDowell, who was tied for 11th going into the weekend, told the PGA website: "I'm sure he knows what he needs to do. Only he knows where he's at in his own mind. We all experience moments of this in our career.
"This is only a mini-crisis. I look at the Match Play as a complete anomaly. He's missed two cuts, big deal. There's a lot of golf left."
Another compatriot to offer support was Lowry, who tweeted: "Gonna put this out there. Rory will win the masters."
McIlroy initially told reporters he was "in a bad place mentally", according to ESPN.
But later released a statement saying: "I sincerely apologise to the Honda Classic and PGA Tour for my sudden withdrawal.
"I have been suffering with a sore wisdom tooth, which is due to come out in the near future. It began bothering me again last night, so I relieved it with [painkiller] Advil.
"It was very painful again this morning, and I was simply unable to concentrate. It was really bothering me and had begun to affect my playing partners."
McIlroy has 14 days to submit written evidence to the PGA to support his claim, with a fine or suspension possible if the body is not satisfied with his explanation.
The link between McIlroy's slump in form and his new clubs has already been speculated on, and although he admitted the change had affected his confidence he had insisted on Thursday following his level-par opening round he was rounding the corner.
Whatever the reasons for Friday's events, playing partner Ernie Els seemd unimpressed by McIlroy's withdrawal.
He said: "I'm a great fan of Rory's, but I don't think that was the right thing to do."
But the South African struck a more sympathetic note as he added: "He's feeling terrible about it, I know he is. That's the last thing he wants to do is walk off.
"Yeah, if he's seven over or whatever he was, you've got something bothering you, [under] the rules of play you can walk off at any time.
"Obviously something was seriously bothering him, and he was not going to make the cut and probably didn't want to continue playing that way."
In McIlroy's absence, the race to succeed him as champion was wide open.
Overnight leader Camilo Villegas signed for a 77 - after a 65 on Thursday - that saw him miss the cut by one shot, a fate barely avoided by Tiger Woods who went round in 70 for the second straight day.
Luke Guthrie emerged from the chaos with a one-shot lead ahead of Michael Thompson following an outstanding round of 63 which put him nine under overall.
Boo Weekley and Graham DeLaet were seven under, while Englishmen Lee Westwood and Justin Rose headed a group of six men on six under.