Morgan Schneiderlin had put Southampton ahead midway through the first half after some sloppy defending, but Stoke battled back to level early in the second period through Mame Biram Diouf.
Hughes' side were then more than a match for their opponents for long spells, and - after his wondergoal against Chelsea a fortnight ago - Charlie Adam scored again to secure all three points with six minutes left, leaving Hughes delighted with a thoroughly professional display.
"I thought their goal came against the run of play," said the Stoke boss. "But we got on level terms thanks to a great finish by Mame.
"And in the second half I thought we were really strong in doing what we were trying to do, we restricted them to few opportunities, and I think the quality of our chances were better.
"We made a few changes and they were effective. Charlie has done it once again - thankfully the ball dropped to him and it's great technique, he knows exactly what he's doing.
"We then needed to manage the game out, and I thought we were a lot better at that today."
