Oldham were convinced that Oxley had made clean contact with the ball, but Lowe picked himself up and sent the keeper the wrong way to give Tranmere a backs-to-the wall victory.
It was their first win of the season, while Johnson's protests saw him sent to the stands.
Johnson said: "We weren't at our best, but the penalty was an unbelievable decision. Nobody even appealed.
"You could see by the way I threw my jacket four rows back into the crowd that I didn't agree with it and now, having seen it on video, I haven't changed my mind.
"It's a horrible way to lose, but you can't legislate for that kind of mistake and I suppose I'll face some sort of punishment myself.
"Maybe we should have had a penalty ourselves in the first half when James Tarkowski was fouled, but you would have to ask the man that matters.
"On another day we would have scored three goals because we whipped some great balls into the box without getting anyone on the end of them.
"And on another day we would have kept a clean sheet, but neither happened and it's so disappointing.
"There were good parts and bad parts to our play, but it's difficult to feel low about the result at the moment because I just feel angry."