Before the game Charlton needed to win all four of their matches to give themselves a chance of a play-off spot, but their season has disintegrated because of their poor home form which has seen them win only eight of 22 matches.
They fell behind after just ten minutes to a bizarre goal when home goalkeeper Darren Randolph, recalled from a loan spell at Bury to replace the suspended Nicky Weaver, could only help the ball into his own net after he collided with his own defender following Stern John's lob.
Charlton failed to produce much sparkle in the first half, the closest they came to scoring were two efforts from on-loan striker Leroy Lita which failed to trouble visiting goalkeeper Richard Wright.
After the break Charlton manager Alan Pardew threw on Andy Gray and Darren Ambrose and the home side began to get on top of their opponents, with first Ambrose firing over the bar and then Lita heading over.
Charlton equalised on 68 minutes when Lee Cook's free-kick was headed into the net by Gray, his first goal since joining from Burnley and the first time he has found the net since he scored two for Burnley against Charlton at The Valley in December.
Saints keeper Wright then made a point-blank range save from Ambrose to keep his side in the game.
In injury time Charlton had two free-kicks just outside the Saints penalty area which they should have done better with.
Jerome Thomas also fired over as Southampton held on grimly for what could be a very important point in their battle to stay in the Championship.