The Potters were presented with a variety of chances right from the start when after only two minutes, John Eustace retrieved the ball with a hard tackle on Claude Davis just outside the area and supplied Gifton Noel-Williams out on the right, but his powerful shot flew wide of the far post.
The Lilywhites best and only real chance fell on 24 minutes when Graham Alexander's free-kick was laid off for Eddie Lewis, but his shot flew straight down the middle allowing Ed de Goey to fist the ball out for a corner.
The driving rain and strong winds made conditions difficult for both sides, but Wayne Thomas took full advantage of this and hit a long-range effort from 30 yards which caught Preston keeper Jonathan Gould off guard, however, he tracked back and did well to palm over the crossbar.
It continued much the same after the break but Preston's counter attack seemed to be stretching City defence and they barely escaped another Lewis free-kick, with the left post saving de Goey's blushes.
North End took the lead in style soon after the 68th minute when forward Healy picked the ball up out at 30 yards and cracked an unstoppable shot that rocketed into de Goey's net.
Stoke tried their best to claw something back and had to wait right until the death when Michael Jackson was spotted to have clashed with Ade Akinbiyi in the box to concede a penalty.
Eustace stepped forward and slotted the ball down the middle to provide the home fans with a fairytale ending.