After some initial confusion, the fan realized the ball had bounced off a tree and dropped into his front pocket.
A rules official gave McIlroy a free drop, and the world's No. 1 player made par en route to a 5-under round that put him near the top of the leaderboard.
McIlory said he was happy to let the fan hand hand over the ball.
"I know how sweaty my pockets are," he said. "I wasn't going into anyone else's."
Kind of reminds us of the scene from Happy Gilmore where Shooter McGavin is forced to hit a ball off a surly fan's foot.
Sadly, Richard Kiel, the seven-foot actor who played the fan, died earlier this week.