Kelvin Wilson scored a late winner as Preston recovered from 2-0 down.
Wilson had a poor start - failing to clear Michael Duberry's long ball, allowing Liam Lawrence to score.
And indecision from Wilson saw Mamady Sidibe head goalwards and then bundle the ball home after Carlo Nash failed to hold it with seven minutes gone.
But Paul McKenna scored from 25 yards, David Nugent converted Simon Whaley's cross and Wilson struck after Steve Simonsen fumbled a cross.
606 DEBATE: Give your thoughts on the match
Preston manager Paul Simpson:
"We had an absolutely appalling start to the game.
"There was a total lack of communication at the back, a total lack of desire
to be ugly and to keep a clean sheet and we gave ourselves a mountain to climb.
"But from that point on we put them under a hell of a lot of pressure by
playing our football and it's a really, really big three points.
"We showed real determination to get back into it and showed our desire and
passion to win the game. All good sides have that passion and hopefully we can go on and prove we are a good side."
Stoke manager Tony Pulis:
"We are desperately disappointed.
"We had a good chat at half-time and I thought we would take it on again but
half-time killed our momentum.
"Preston got hold of the ball and the first and third goals were really
"That gave them the advantage and once they got one back we weren't able to
keep hold of the ball.
"Our front two had been such a handful in the first half but were anonymous
in the second and then to cap it all the third goal was poor goalkeeping by Steve Simonsen."
Preston: Nash, Alexander, Chilvers, Wilson, Hill, Lewis Neal, Sedgwick (Whaley 59), McKenna, Pugh, Nugent, Ormerod (Ricketts 88).
Subs Not Used: Lonergan, Dichio, St. Ledger.
Goals: McKenna 65, Nugent 74, Wilson 89.
Stoke: Simonsen, Wilkinson (Brammer 77), Duberry, Higginbotham, Griffin, Hoefkens, Matteo, Russell, Lawrence, Sidibe, Pericard (Rooney 83).
Subs Not Used: Eustace, Sweeney, Dickinson.
Booked: Wilkinson, Simonsen, Hoefkens.
Goals: Lawrence 2, Sidibe 7.
Ref: R Beeby (Northamptonshire).