A second string Potters side left it late but did enough to come away from the welsh town with a victory.
The Potters sent quite a strong line up to the game, seeing as the 'first team' were at Wrexham at the same time with eight players who have played Premier League football in the starting eleven.
Despite the visitors dominating the game, with five efforts cleared off the line, aswell as the home keeper being forced into numerous top saves, it took until the 86th minute for City to score, Matthew Lund rising highest to power home a header and take the spoils.
Attentions now turn to the Potters opening day Premier League fixture, a Staffordshire derby at Wolves, next Saturday.
Stoke(4-4-2): Nash; Wilkinson, Dickinson, Shotton, Pugh; Soares, Tonge, Lund, Marshall; Kitson, Beattie