Sam Allardyce can thank Henrik Pedersen for keeping his dream alive of leading his team into the Carling Cup final.
Despite having the vast majority of the play, Wanderers could not break the deadlock within the 90 minutes with Saints keeper Antti Niemi keeping his team in the match.
It was deep into the second period of extra time when the Dane put Bolton through to the semi-final.
Straight from the off the home side went on the attack and after only two minutes Pedersen met a fine cross, the resulting header being cleared off the line.
Minutes later Saints keeper Niemi was forced to make an instinctive low dive from a well-drilled free-kick from Jay-Jay Okocha.
Wanderers kept up the pressure with former Southampton striker Kevin Davies trying to menace his former team-mates.
The home side felt they should have been awarded a penalty after Pedersen appeared to be felled in the penalty area.
Saints though put up a resiliant defence and later in the half found some space up front themselves and a Paul Telfer shot grought a good save from Trotters keeper Kevin Poole.
Despite having less of the ball, the visitors were unlucky when Fitz Hall flicked the ball the wrong side of the post from a late first-half corner.
The second half went as the first, with the home side dominant.
Niemi almost single-handledy kept his side in the cup with excellent saves from Nicky Hunt, Okocha twice in two minutes and when Bruno N'Gotty got the simple job of toepoking the ball home, the keeper quickly took the ball off the Frenchman's foot.
On 90 minutes Poole saved well from a Brett Omerod shot and then Okocha had to kick the ball off the line in injury time.
And so to extra time and by now the home team looked to have little left with Saints keeping the ball for long periods.
The breakthrough came on the Bolton right when Ibrahim Ba crossed the ball for Pedersen to poke the ball home and put his team into the semi-final.