The Republic of Ireland striker spent one season at the Racecourse Ground in the 2005-06 season, and his second-half goal proved to be decisive in a game of few chances
Former Dragons forward Jonathan Walters scored the winning goal early in the second half to seal victory for Mark Hughes' side in a match lacking clear-cut chances.
Ireland international Walters met a Charlie Adam cross at the front post in the 51st minute and scrambled the ball under Joslain Mayebi.
The Premier League side controlled large parts of the game at the Racecourse Ground but were unable to turn their dominance into more goals.
Jermaine Pennant, starting his second game of pre-season, threatened from the right-hand side and delivered some dangerous crosses for Peter Crouch, but the striker was unable to convert them.
Stoke's best chance before Walters' strike came through Matthew Etherington, but the winger blazed his shot over the bar from close range after good build-up play from Crouch.
Asmir Begovic was rarely tested by the home side, veteran striker Brett Ormerod looked most likely for the non-league outfit but failed to seriously trouble the Bosnia and Herzegovina international keeper.
Stoke have one friendly game left, against Genoa, before they begin their Premier League campaign away at Liverpool on August 17.