City were made to suffer by a clinical Liverpool side at Clayton Woods Training Centre.
Two late, late strikes added to a first half opener to see the three points travel back to Merseyside.
Without key players Louis Moult and Rodney McDonald the hosts were on the backfoot for long spells in the first half as they struggled to get into the game. The visitors were able to keep the ball but had very little penetration themselves creating very few chances.
The first chance arrived on 12 minutes but after a deep ball into the box found an unmarked midfielder he hurried his effort and the ball flew well over the bar.
The next opportunity on twenty four minutes was taken though as the lone striker for Liverpool bulldozed his way through the home defence, with nobody putting in a strong enough tackle, before sliding it past Parton and into the bottom corner to open the scoring.
The Potters first, and only, opportunity of the half arrived shortly before the break when a Wint cross from the left was flicked on by Alexander. The keeper punched the loose ball but only half cleared it to Nicholls. The energetic midfielder struck his shot low and hard but a brave block diverted it away from the net.
Following that poor half the hosts came out with much more purpose and had the Reds on the back foot for long spells in the second half, with cross after cross and numerous set pieces seeing Liverpool camped inside their own box and Stoke went close to an equaliser a number of times. Urwin just failed to collect Nicholls pass that put him through on goal, Alexander headed Urwin's cross narrowly wide whilst the target man lashed over after the ball fell at his feet following a scramble inside the area.
City did manage to get the ball in the net on 64 minutes when, after a corner was half cleared, Jackson clipped the ball back into the area. Foster watched the ball over his shoulder before smashing a left footed volley over the keeper and into the top corner. Just as the defender started to celebrate the offside flag was raised and the goal chalked off.
The equaliser seemed just around the corner and City thought they had it on seventy three minutes when Nicholls burst forward. Carrying the ball into the area he burst past two desperate tackles before unleashing a thunderous drive across the keeper. With the ball looking to nestle in the net the post came to the Reds aid and the ball rebounded off the upright to safety.
With thirteen minutes left a double replacement saw defender Cohen moved to the lone striker role for Stoke and he immediately collected Nicholls pass, played a one two with Harrison before firing in a shot at goal. The effort was straight at the keeper though and was easily saved.
As the Potters poured forward Liverpool secured the win when a weak back pass was seized upon and knocked past Parton before a penalty was awarded in the dying moments. Foster tugged the shirt of a striker as he looked to shoot and although keeper Parton saved the penalty the rebound was knocked into the opposite corner to condemn the Potters to just a third home defeat this season.
Under 18's(4-5-1): Parton; Hedley, Cohen, Connor, Wint; Jackson(Stockhall 77), Mitchell, Nicholls; Urwin, Vickers(Foster 30), Alexander(Harrison 77)
City are next in action on Saturday when they travel to Huddersfield for their final away game of the season whilst the next home game is next Wednesday when the Potters take on Manchester United, kick off 1pm.