The 2014 champion at the Wentworth venue eventually signed for a five-under par 67, two strokes behind leader Matthew Baldwin.
"I don't think it's ever happened to me before," McIlroy said of the incident on the par-five 12th, when his approach finished six feet from the hole despite the clubhead flying off at impact.
"I hit nine iron on the ninth hole and it looked as if the ferrule (fastening) was coming loose, but it was actually the head detaching from the shaft.
"I obviously didn't realise that when I hit the shot on 12. It was a bit of a weird feeling. Thankfully the ball went where I wanted it to. It could have been a lot worse but thankfully got it repaired and got it back on the 16th."
The Northern Irishman also had to putt left-handed at the eighth after his ball landed on the edge of a pond.
"Hit a left-handed putt and did a decent job. At least I got the speed pretty much correct. I didn't get the line right, but knocked that one in, made par," he said.
Baldwin, who won his first European Tour title in South Africa last year, admitted he often struggles with nerves but was delighted with the way he remained focused in front of the large crowds.
"That's a rarity for me to be fair, my thoughts are usually running wild," the 38-year-old said.
"It's something that I'm trying to work on. I had a focus point of trying to make a good strike on the golf ball and take it from there."
Baldwin has a one-shot lead over British Masters winner Niklas Norgaard and Belgium's Thomas Detry, while McIlroy's 67 was matched by Ryder Cup team-mates Shane Lowry and Robert MacIntyre, with 2019 winner Danny Willett returning a 68.
The former Masters champion underwent shoulder surgery after this tournament last year and has only played eight events in 2024, making the cut at Augusta National but missing the cut in each of his last five starts.
"It's been tougher than I thought," Willett admitted after a round containing six birdies and two bogeys.
"The first six months when I wasn't doing anything was phenomenal. Just sat on the sofa, go to the gym every day but zero pressure - it could take as long as it wanted to.
"I think once I started getting back into trying to get ready to play, we just realised how insane this game drives you."
He added: "I played Augusta because conditions were perfect for me to have a chance. It was firm, it was fast, it was windy, but then other tournaments I've played I've obviously not performed and not taken much from.
"When you're trying, working, doing everything you think is right and shooting 75, it's hard to take the positives from it."
