The Lilywhites went down to ten men early in the second half when Ben Pearson was shown a straight red card - his third of the season - for bringing down Patrick Bamford when through on goal.
A few minutes later Bamford opened the scoring for the Whites with a ferocious 25-yard effort, and the same man doubled the visitors' tally with a header 14 minutes from time, a result which edged Leeds back into the top two.
Following the 2-0 loss, Johnson admitted that the Pearson dismissal was a game changer but claimed that his earlier booking was not warranted, saying the likes of Luke Ayling were not getting punished with challenges "just as bad".
"I thought Ben’s first yellow card was a bit harsh," Johnson, who joined PNE from Aston Villa in 2015 and has made close to 200 appearances for the Lilywhites, is quoted as saying on their official website.
"A few of their lads were putting in challenges that were just as bad like the one on Josh Earl from Luke Ayling but they weren’t getting yellow cards but we’ve just got to get on with it. That’s part of the game, you’re going to get good days and bad days like that. We’ve just got to put it behind us now and go again on Saturday."
The defeat sees Preston finish the day 11th in the Championship table ahead of Wednesday's games and their weekend trip to West Bromwich Albion, while Leeds are up to second ahead of Sheffield United's trip to Birmingham City.
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