Stoke's surprise win over Manchester United last time out seemed to have really rejuvenated the Potters, who were vastly improved once again.
With only one win on the road all campaign, expectation wasn't high, but Hughes' side attacked in numbers and caused a real threat, especially in the first half.
Southampton twice led through Rickie Lambert and Steven Davis, with Stoke responding through Peter Odemwingie and Peter Crouch.
"It was an important game for us," Hughes said.
"Obviously we had a fantastic result last weekend against Manchester United and it would have been a real disappointment not to have got something out of this game because it is important we get a run going.
"I felt we were the better side in the first half, albeit we went behind twice, but we showed great character and no little skill to get back on level terms.
"In the second half, both teams cancelled each other out somewhat and as the away team that's a very good performance from our point of view.
"They're a team I've enjoyed watching this year and we restricted them to very few clear-cut chances. That shows the quality of our performance."
Charlie Adam was again key for Stoke, following up his winner against United by providing the assists for both goals at St Mary's - the first a particularly impressive through-ball for Peter Odemwingie to net.
"He's got that, we all know that," Hughes added.
"What we have now is a little bit of difference in terms of our attacking threat.
"Peter Odemwingie has joined us and he's an experienced Premier League player and we've talked about him exploiting that space in between centre-backs behind full-backs and Charlie, given his range of passing, will always put people through."