Pennant was released by the club in the summer but was brought back by Hughes, and the former Liverpool man repaid the faith by scoring his side's winner against West Ham United.
"I'm grateful to the club, the gaffer and the fans for the faith they've shown in me," he told the club's official website.
"It's funny in football how things can turn; I'm now enjoying my football so much and the goal against West Ham means so much to me.
"I dedicate the goal to the fans because they have always been brilliant towards me and the rest of the boys."
Stoke have taken six points from their opening three Premier League games this season.