Pennant will report for duty with the rest of the squad on Monday after Hughes made offering the winger a new contract the first major decision of his reign.
The manager said: "He was out of contract and on the list of players who weren't going to be retained.
"I looked at that and thought 'Would I be upset if I saw Jermaine Pennant in someone else's shirt?'
"The answer to that was a very clear 'yes'. It didn't make sense to me to allow him to leave the club.
"He has a real affinity with Stoke and the supporters and he loves playing in the shirt.
"He wanted to stay and I wanted to keep him so it was quite an easy decision."