A late comeback from the Robins was not enough to take Town's Carling Cup second round tie beyond the 90 minute stage on a frustrating night at The County Ground.
Mehdi Kerrouche, a first half substitute, scored a late free-kick but the goal was not enough to keep Town in the competition. Paolo Di Canio made two changes to the starting side with Alan Connell and Alberto Comazzi coming into the side to replace Raffaele De Vita and Joe Devera.
Town started the game brightly but the visitors soon imposed themselves on the game with a slick passing display. Forte's run down the right was met by Lallana with just eight minutes on the clock and the frontman sidefooted just wide. Former Town loanee Lee Holmes played a part in the Southampton opener on 16 minutes as he crossed for Guly Do Prado who headed home from close range.
The Saints continued to press with Dan Harding next to go close before the visitors extended their lead. A through ball from Do Prado was met by Jonathan Forte who fired in a shot which had the beating of Phil Smith and rolled into the net. Di Canio responded by making his first change of the game with Kerrouche coming on in place of Connell in the frontline. The Robins then rallied with Matt Ritchie firing in a low cross which Aden Flint almost got on the end of with the half-time whistle looming. Di Canio made no changes to the side at the break and the Robins emerged for the second period with renewed vigour.
A deep cross from Lander Gabilondo was met by Clarke and he headed wide from the edge of the six-yard box.
Di Canio then introduced Etienne Esajas into the action with Gabilondo making way, and the substitute almost made an instant impact with a low drive which was gathered well by Bialkowski. Phil Smith was forced into a smart stop at the other end with Frazer Richardson's powerful effort testing the Town stopper. Simon Ferry then headed Callum Kennedy's free-kick wide of the post with the home side still pushing to get back into the affair which had largely been dominated by a competent performance from the visitors. Di Canio's final change then saw Alan McCormack introduced into the midfield replacing Simon Ferry.
Kerrouche's moment then arrived. Following a foul on the Algerian on the edge of the box, Kerrouche stepped up and curled in a superlative free-kick past Bialkowski into the top corner in front of the Town End with ten minutes remaining.
However, Saints substitute Rickie Lambert capped the win for his side after latching onto a through ball. He evaded the challenge of Flint before rounding Smith to fire into the net to seal the Saints' place in the third round.
Full-time: Swindon Town 1 Southampton 3