The Irishman was informed on the 15th hole by an R&A rules official that the incident on the par five 12th at Royal Portrush was under investigation after footage started to emerge on social media.
Lowry shot a second-successive 70 to sit two under for the tournament but was subsequently docked two strokes, leaving him one shot inside the cut line and 10 behind leader Scottie Scheffler, after being asked to look at the video evidence.
Although his club did not touch the ball slow-motion footage appeared to show he hit a blade of grass which moved it.
"I didn't know anything happened until walking up the 15th fairway and then the rules official came over and told me that there was a possibility the ball moved on the 12th for my second shot," said Lowry.
"I've asked him 'How many shot penalty is that if it did?' and he said 'Two'. Obviously then I feel like I'm on the cut mark then, which is not very nice. I feel like I played well on the way in and then obviously waited to see.
"I was in there with the rules official and wasn't arguing my case but I'm disappointed that they don't have more camera angles on it.
"The one zoomed in slow motion - they're trying to tell me if it doesn't move from the naked eye, if you don't see it moving, it didn't move.
"I told them I definitely was looking down towards the ball as I was taking that practice swing and I didn't see it move.
"I'm still not sure, to be honest, whether it was or not, but I had to take the penalty because I can't have my name talked about or tossed around like that.
"It's obviously very disappointing. I felt like I played really well today and that's hard to take.
"I'll just have to dust myself off and get out there tomorrow and give it a go."
A statement from the R&A read: "It was clear that the ball moved immediately after the player's club touched foliage close to the ball during a practice swing and that the player's actions caused the ball to move.
"In these circumstances there is a one-stroke penalty and the ball must be replaced.
"However, as the ball was played from the spot where it was moved to, the player played from a wrong place and incurs a total penalty of two strokes."
12°C