Latics dominated the first half of the clash but a lucky strike from Stuart Beavon and a Kevin Davies penalty, his first for his new club, had the hosts two goals to the good at the break.
Joseph Mills, James Tarkowski and Adam Rooney all came close for the visitors in the first half and while Preston had their moments after the break it was still Oldham who looked the more threatening.
But it was only in the 83rd minute that they finally got their reward, Tarkowski heading home from a corner to provoke a frantic finish but Preston held on, much to Johnson's disgust.
"I'm not sure how we've not won the game. We've controlled the whole match, but for probably 15 minutes," he said.
"We've probably lost that game from not having the bravery to quite take our chances. We started really well, they've scored a goal out of nothing, we had a few chances and then one stupid mistake for the penalty and it's 2-0 to them at the break.
"I thought we started the second half well, we dominated the half again, the lads kept going and put in a terrific shift but we just couldn't score.
"We've created 18 chances against a team like Preston and to come to a place like this and do that is brilliant from us.
"Their fans have clapped us off the pitch and that's nice to know but yet again it's another game where we haven't got three points and we've got to change that.
"We've looked great, we've passed the ball brilliantly at times and if we can start taking our chances then I'm sure we'll be fine."
And Preston boss Simon Grayson admitted his side had been lucky to grab the win that maintains their unbeaten start to the League One season.
"It was a tough game and we knew that was going to be the case. We were made to work very hard and they created some good chances in the first half," he said.
"They kept possession well and didn't allow us much of the ball and that meant we had to dig in and head balls in and around our 18-yard-box and battle hard.
"We know that we can play better than that. We need to do better without the ball than we did but we've got three points, we're still undefeated and we'll go into the top six with that result.
"It's good for us that both of our strikers are off the mark and hopefully they'll be a few more.
"That was probably our toughest game this season with the way that they play."