The 2019 champion got off to a fine start at Royal Troon on Friday with three birdies on the front nine to go to seven under.
But all his good work was at risk after he fired deep into bushes off the left on the 11th.
Lowry then hit a perfect provisional onto the green only for his original ball to be found by a spectator.
The world number 33 was forced to identify his ball, take a drop and ended up being happy not to have his whole tournament torn apart by one stray shot.
"I hit a great provisional. The referee asked me going down, 'did I want to find my first one', and I said 'no'. So I assumed that was okay. Then we get down there, and somebody had found it," Lowry told a press conference.
"I thought, if you declared it lost before it was found, that you didn't have to go and identify it.
"To be honest, I was happy enough leaving there with a six. It wasn't a disaster. I was still leading the tournament."
Lowry showed remarkable poise to steady the ship with four straight pars before recovering the two lost shots in the final three holes.
The 37-year-old pulled away from the field during his third round at Portrush en route to his only major victory five years ago and is comfortable with the idea of being in the final group heading into the weekend.
"I wouldn't say I'm a good runner," joked the burly Irishman, who weighs in at over 100 kilos, when asked if he is a good front-runner.
"I put myself there in a few big tournaments, and I've managed to knock them off. So I've done it a few times. I don't know. It's hard to win tournaments. We'll see. I'll tell you Sunday evening."
World number one Scottie Scheffler appears the major threat to Lowry on the leaderboard.
The American moved to within five shots of the lead on Friday despite making a bogey at the 18th.
"I'm not sure Scottie Scheffler is too worried about anyone with the form he's in," said Lowry of the man who has already won six times this year.
"He's obviously on the leaderboard, and he's one person that people are going to be talking about."
