The Republic of Ireland international capitalised on the run of the ball when a clearance fell into his path and gave Bart Bialkowski no chance with a cool finish.
Town matched the Premier League opposition for long periods in a game of very few chances in front of 27,933 fans but couldn’t breach the visitors’ defence, with David McGoldrick adding to Town’s concerns when he limped off in the second-half.
Town made just one change to the side that drew at St Mary’s in the first game, former Saint Bialkowski coming in for the injured Dean Gerken.
The biggest crowd at Portman Road since the Carling Cup semi-final against Arsenal four years ago were in attendance as Blues started brightly, Stephen Hunt sliding the ball past Fraser Forster and into the net but not before the offside flag was raised.
Victor Wanyama sent a 40 yarder over the bar after Bialkowski’s clearance had landed at his feet, then at the other end Jonathan Parr’s cross was gathered by Forster as Daryl Murphy looked to capitalise on any mistake.
It was Saints who got the breakthrough though on 19 minutes. Dusan Tadic’s clever backheel released the supporting James Ward-Prowse, Luke Chambers
intervened with a terrific challenge but the ball broke to Long who passed it into the net with a first time finish.
Town responded with McGoldrick firing over, then the frontman tried to release Murphy but Jose Fonte stopped the danger, while at the other end Ward-Prowse sent a long ranger onto the roof of the net.
Darren Ambrose sent a cross just too high for McGoldrick after a surging run down the right flank, then put in an even better delivery that looked destined for Tommy Smith until Florin Gardos cleared.
McGoldrick cannoned a free-kick into the wall as Town pressed for an equaliser leading up to the break, Smith and Christophe Berra smothering a shot from Long as Southampton threatened to extend that lead.
Saints made a change at half-time with the injured Wanyama replaced by Steven Davis and it was the visitors who threatened in the first exchanges of the second-half, Tadic’s cross fed back into the box but Smith cleared.
Berra did well to prevent Long getting in, then Town made a first change with Tyrone Mings on for Hunt. The former Southampton Academy player immediately in the action with a cross that was met by Ambrose whose header was saved by Forster.
Murphy’s cross was put behind by Nathaniel Clyne, before Blues made a second change with McGoldrick limping off to be replaced by Balint Bajner just past the hour.
Long was robbed by Chambers as he tried to wriggle free inside the box, Saints then withdrawing the dangerous Tadic, leading scorer Graziano Pelle joining the action.
Kevin Bru fired over, Town then making a final throw of the dice with Cameron Stewart introduced for his home debut 10 minutes from time but
Southampton held firm to book their place in the fourth round.