Saints took an early lead through a wonderful Rickie Lambert free-kick only to be pegged back by Peter Odemwingie's first goal for Stoke, who had gone 369 minutes without netting away from home before that.
Steven Davis' fortuitous effort saw Saints retake the lead soon after but they again relinquished control when former Southampton frontman Peter Crouch bundled home.
The result brought an end to Stoke's four-game losing streak away from the Britannia Stadium and was a decent follow-up to last weekend's 2-1 win against Manchester United.
Hughes said: "It was an important game for us. 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 Odemwingie to net.
"He's got that, we all know that," Hughes said of the Scotland midfielder. "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."
- Sports & Recreation
- Peter Odemwingie
- Manchester United
- Rickie Lambert
- Peter Crouch