Andy Gray's equaliser earned Charlton a point but the striker's first goal for the club may not be enough to sustain the Addicks' push for the play-offs.
Southampton took the lead via a Patrick McCarthy own goal.
Goalkeeper Darren Randolph gathered Stern John's hooked shot but dropped the ball as he fell on McCarthy, who then directed the ball into the net.
Substitute Gray then levelled when he headed Lee Cook's corner beyond Southampton's Richard Wright.
• Charlton manager Alan Pardew:
"It looks like it might have cost us although mathematically it is not over.
"I can't keep making excuses for our failure to win at home, but I think I know why and I have to put it right.
"I have told the players that over the next three games they have to show me they want to be here, otherwise I will make changes."
• Southampton boss Nigel Pearson:
"Alan might think they should have won but I thought we deserved something out of the game.
"It was two sides doing all they could to get the win. It was a pretty committed game from both sides, my team have had a real go and I can't criticise them.
"It's another point which edges us closer but there is still lots of work to be done."
Charlton: Randolph, Halford, Bougherra, McCarthy, Thatcher, Zhi (Thomas 78), Semedo (Ambrose 46), Holland, Cook, Iwelumo (Gray 46), Lita.
Subs Not Used: Elliot, Varney.
Booked: Semedo, Bougherra.
Goals: Gray 69.
Southampton: Richard Wright, Jermaine Wright, Perry, Lucketti, Surman, Idiakez (Viafara 70), Euell, Safri, Licka, John (Pericard 79), Wright-Phillips (Saganowski 75).
Subs Not Used: Davis, Powell.
Booked: Jermaine Wright, Wright-Phillips, Perry.
Goals: McCarthy 11 og.
Ref: Andy Hall (W Midlands).