City were beaten by a late goal for the second time in two days after succumbing to a Adam Mekki goal.
The Potters put out a largely second string side, with midfielder Soares and defender Shotton up front, but still managed to control large periods of the game.
Stoke went close to breaking the deadlock ion the first period, Diao twice heading inches wide, Pugh testing the home keeper and Shotton seeing his shot cannon back off the far post. Sorensen, making his first appearance of pre-season, was required at the other end but wasn't too pressed with a couple of long range efforts.
The second half was more stop start due to numerous substitutions, including Stoke boss Tony Pulis' son Anthony coming on for Aldershot, but Diao and debutant Woodgate both went close for Stoke.
Woodgate played 61 minutes before being subbed and looked in impressive form, winning every header and also carrying the ball out of defence well before being replaced by Huth.
The deadlock was broken on 81 minutes when Mekki saw a shot blocked but then got hold of the rebound and slotted past Nash, on for Sorensen at half time, from the edge of the box.
City pressed for an equaliser, trialist Stambolziev looking dangerous again, but couldn't put the ball in the net and were left trying to forget a nightmare 24 hours and look forward to Thursdays Europa League qualifier with Hajduk Split.
Stoke: Thomas Sorensen (Nash 45), Andy Wilkinson, Carl Dickinson, Diego Arismendi, Salif Diao, Jonathan Woodgate (Huth 61), Michael Tonge, Danny Pugh, Ryan Shotton, Tom Soares (Stambolziev 72), Ben Marshall (Wilson 61)
Subs not used: Matthew Etherington, Kenwyne Jones