The Potters boss admitted that he was disappointed with the result, but drew positives from his team's improved performance in the second half against a side who hammered Sunderland 8-0 last weekend.
Hughes told reporters: "We are disappointed to a certain extent because in the first half we were a little bit apprehensive in our play, maybe a consequence of Southampton's great result last time out.
"We showed them too much respect. We conceded from a set play, where the ball was ricocheting around. We were unlucky that it fell to one of their guys and he despatched it.
"We were better second half, got a little bit of control of the game, and you saw by the reaction of the Southampton crowd at the end that they knew we were pushing to get back on level terms."
The result took Southampton to second place in the Premier League table, while Stoke remain in 11th.