He ended up with a bogey there after taking a penalty drop, hitting his fourth shot on to the green and two-putting for a six.
The four-times major winner was level par for the day at that point and went on to card a two-under 70 on the challenging Blue Monster course at the Trump National Doral Resort.
"Frustration got the better of me," McIlroy told Golf Channel about his club toss after posting a one-under total of 143 in tricky scoring conditions. "I've been sort of fighting that miss (to the left) basically for the last couple of weeks.
"It wasn't something that I would encourage anyone to do. I wouldn't encourage kids to do it if they were watching on television. It wasn't very role modelish of me.
"It felt good at the time but right now I regret it. I walked away with a bogey but was able to re-group and shoot a decent score."
McIlroy, who missed the cut at last week's Honda Classic in his first PGA Tour start of the year, mixed six birdies with four bogeys for a roller-coaster round, ending the day eight shots off the lead.
"Mentally it was a bit of a grind," said the 25-year-old, who won his fifth European Tour title at the Dubai Desert Classic last month. "I was getting frustrated at times.
"I got off to a good start and then to give those shots away ... it felt like any time I took a couple of steps forward, I was taking one step back.
"Nice to finish under par, nice to move up the leaderboard a little bit but I've got some work to do on my game if I want to contend this weekend."
McIlroy, who was left with just 13 clubs to complete his second round, is almost certain to be penalised for his public demonstration of anger, though the PGA Tour has a policy of never announcing details of fines.
(Reporting by Mark Lamport-Stokes in Los Angeles; Editing by Gene Cherry)
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