Danny Swanson fired Peterborough ahead after 18 minutes with a curling shot into the bottom corner but North End levelled on the stroke of half-time through Neil Kilkenny.
Preston then sealed the points through Joe Garner's double - he tapped home in the 80th minute after Paul Gallagher's shot had hit a post before slamming home into the roof of the net in the closing stages.
Victory saw fifth-placed Preston stretch their lead over Peterbotrough, who remain sixth, to 14 points but with second-placed Brentford seven points clear with two games in hand, North End look destined for the play-offs.
With MK Dons slipping up at home to Gillingham, Peterborough remain three points above seventh place and have a game in hand over their close rivals.
But Ferguson believes his side were found out at Deepdale.
"I thought the first two goals we conceded were really poor and you can't be that sloppy," he said.
"I'd have to watch the game again. I was happy with some parts of what we did and not in others.
"We caused them all sorts of problems with our system in the first half but we just didn't keep at it.
"We're a team that's not the most physical, we pride ourselves on technical skills and on a pitch that good we had a real chance, but we just weren't good enough.
"They're a good team Preston, they have only had five defeats.
"Joe Garner is a good player who has been fantastic for them this season - the front two of Preston kept them in it at times.
"We're clinging on to the play-off places at the minute but that's all we're doing.
"We've had 16 defeats and that is too many in a season."