Pennant produced a wonderful 82nd-minute strike that curled over the wall and beyond goalkeeper Jussi Jaaskelainen to secure a 1-0 victory in their Barclays Premier League clash at Upton Park.
The 30-year-old winger's contract was due to expire in the summer and he was expected to leave having been marginalised under former boss Tony Pulis, only for Hughes to give him a 12-month extension.
"Jermaine has been excellent since I came to the club. I've always admired his talent, but he's had his own problems and will tell you that himself," Hughes said.
"When I came in and there was a real possibility he could leave the club, I felt like I couldn't allow that to happen. You don't want him turning up at Stoke in a different shirt.
"I felt it made sense to keep him at the club and work with him to see what he's like as an individual and player. He hasn't disappointed me. He comes in every day with a smile on his face.
"His work's good and you don't score a goal like he did without putting extra work in on the training ground, which he does every single day.
"In the past maybe he's been judged before he's had the chance to show what he can do. He's let himself down probably as well, which he'll admit to.
"He's in a different place in his life now and is enjoying his life. I'm delighted for him."
Pennant's goal was the highlight of a frustrating match that dominant Stoke should have won more comfortably with Kenwyne Jones, Marc Wilson and Jonathan Walters failing to convert first-half chances.
"I think everybody would agree that we deserved to win," said Hughes, who is hoping to bring in an attacking player before the transfer window closes on Monday.
"From the first minute until the last we got the ball down, passed and moved. Overall we always looked a threat and the only criticism I'd have is we should have won more comprehensively.
"We had to wait until the latter stages of the game and that great finish from Jermaine, but from our point of view it was almost the perfect away performance."
West Ham manager Sam Allardyce acknowledged it was a poor display after watching his side fail to seriously trouble Stoke keeper Asmir Begovic.
"At home, I haven't seen us play that badly since we've been back in the Premier League, sadly," Allardyce said.
"We have to accept that at this moment in time it looks like we're still establishing ourselves in the Premier League.
"We still can't quite reach the level of consistency this league demands. It was a really off day for us, a bad day. Our back four limited Stoke very well.
"But the front six in terms of creativity really wasn't there. It really wasn't good enough and we played poorly, individually and collectively."