A controversial penalty deep into stoppage time by James Beattie eased the pressure on beleaguered manager Paul Sturrock and gave Saints a win they scarcely deserved.
Beattie, a former Blackburn striker playing against his old club, smashed home the spot kick after Craig Short had bundled him over in the area as they contested a centre from the right by Paul Telfer.
It was rough justice on Blackburn who had played a full part in an exciting last half an hour and were looking good value for a draw until Beattie tumbled in the box.
Sturrock went into the match knowing his grip on the managerial seat at St Mary's was only tenuous and Beattie's late winner will at least have delayed his sacking, if not secured his job.
It was a subdued and tense St Mary's and the match only sparked to life near the end, four goals coming in the final 22 minutes and with enough excitement to make up for the tepid first hour.
Sturrock made four changes from the team beaten at Aston Villa last week while Graeme Souness made three after a disappointing display at West Brom on the opening day.
Southampton went ahead after 32 minutes when a centre from Fabrice Fernandes from the right eluded the Blackburn defence for the alert Kevin Phillips to stab in from close range.
But Blackburn were level in the 50th minute when Paul Dickov, who came off the bench at half time to star for Blackburn, fed through a pass for Barry Ferguson to score with a left-foot shot.
Brett Emerton showed tremendous pace and skill down the right in the 68th minute to get in a centre which found Dickov unmarked and with time to turn and shoot into the roof of the net from close range.
Brad Friedel made a great save from Phillips four minutes later and Southampton began to show the spirit for which Sturrock so desperately hoped, paying off with an equaliser two minutes later.
Beattie got down the right and when his centre went across the face of the goal without anyone able to touch it, it came to Fernandes on the left.
The exciting winger touched a pass to Anders Svensson whose right-foot shot drifted away from the goalkeeper and into the roof of the net.
Svensson went the whole of last season without managing to get on the score-sheet and the relief around the ground was clear to see although Antti Niemi was immediately required to make a great save to keep out Dickov.
Blackburn began to lose their calm under pressure and Dickov, Michael Gray, Nils-Eric Johansson and later, Ferguson, were all booked.
At least Ferguson had grounds for complaint, kicking the ball away in fury and frustration when the penalty award was given against the side he had led so ably.
Beattie's penalty, drilled to the goalkeeper's left as Friedel moved to his right, proved to be the winner, as Saints snatched an unlikely victory.
Phillips was outstanding up front for Southampton but Sturrock's side owed as much to their goalkeeper Niemi, who made a tremendous save from Jon Stead in the 11th minute and was a steady figure behind a shaky defence.