The Englishman got on the end of Nathan Redmond's cross to nod home the winner for Saints. It was the south coast club's first win for the season.
Both sides made 10 changes to their starting line-ups from the weekend's Premier League action.
Speaking after the game, Brighton manager Chris Hughton believed his side lacked a moment of quality to snatch the victory.
He said: "I couldn't fault the players - the game looked like it was going to be a draw, and it was going to take that little bit of quality to change that.
"We got into some really good areas and created chances - Viktor's [Gyokeres] header was probably the best chance we had. They had a similar chance and scored it.
"It was always going to be that one moment that changed things, and unfortunately it came for them.
"The big disappointment is that the game was heading for a draw, and that really would have been a fair result."