Pierre-Emile Hojbjerg gave Saints the lead at St Mary’s with a stunning long-range effort 10 minutes before half-time.
And they made it 2-0 midway through the second half thanks to a penalty from Danny Ings.
But two minutes later Brighton pulled a goal back through Shane Duffy’s header and the Seagulls were level in the 91st minute when Glenn Murray scored from the penalty spot – his third goal in as many games against the Saints.
It was also the third straight league draw between the sides.
The result left Southampton and Brighton 13th and 14th in the table respectively, the Saints just ahead on goal difference.
Mark Hughes’s men took a spectacular lead in the 35th minute.
Brighton headed a cross out from the penalty area and the ball fell to Hojbjerg.
From fully 30 yards out, the Dane let fly with a powerful shot into the bottom corner, the ball swerving in late from just outside the post. It was a strike that gave Mat Ryan, Brighton’s Australian goalkeeper, little chance.
The Saints doubled their lead in the 65th minute when, after a poor challenge by Gaetan Bong on Ings in the box, Ings himself scored from the ensuing penalty with a low strike past the right hand of the diving Ryan.
But barely two minutes later, Brighton, who came from 2-0 down to draw 2-2 with Fulham last time out, were back in the game.
No Southampton defender made a move to cut out a long free-kick into the box and Seagulls centre-back Duffy headed in unchallenged from six yards out to reduce the home side’s lead to 2-1.
It seemed Southampton would see the game out but in the closing seconds of normal time Chris Hughton’s men were awarded a penalty after James Ward-Prowse shoved Duffy over inside the box following a Brighton corner.
Referee Anthony Taylor pointed to the spot without hesitation and Duffy made no mistake.
There was still time for Southampton to launch one last attack but Ryan made a fine save to deny Ryan Bertrand.