Martin Jol's side came back from a goal down only to surrender their slim lead in the final minute of normal time with the giant Portuguese defender grabbing his second of the game
Enjoying a period of sustained possession early on, Southampton took an early lead through a Jose Fonte header at the near post from an accurate Adam Lallana corner.
However, having already thrown away nine points in the top flight from winning position so far this term, they resorted to type in the second half when Jos Hooiveld turned in a stinging strike from John Arne Riise into his own net to bring the scores level.
With the second half much more open than the first, Fulham took the lead for the first time through Kieran Richardson late on after converting Sascha Reither's excellent low cross, but Fonte responded by nodding in his second of the game in the final minute of normal time.
Southampton boss Nigel Adkins made three changes to the side which lost their last league outing against Everton, with Gaston Ramirez and Nathaniel Clyne both missing out with dead legs and James Ward-Prowse dropping to the bench, with Daniel Fox, Jason Puncheon and Morgan Schneiderlin all starting instead.
Fulham manager Martin Jol made just one change to his team, with Alexander Kacaniklic coming in for Mladen Petric who was ruled out with a calf complaint, while the match came a little too soon for Dimitar Berbatov, who didn't even make the bench as he sits on the sidelines with a hip injury.
After a bright start from the hosts, their pressure told in the 4th minute when Fonte managed to guide in a deft header into the far post after a pacy inswinging Lallana corner on the right.
With Fulham dominating possession but creating little with it, Puncheon had an effort cleared off the line moments later and then a goal chalked off for fouling Mark Schwarzer after a series of dangerous set-pieces, but they went in at the break a goal ahead.
Trying to put a lacklustre opening half behind them, Fulham went close to troubling the scorers on the hour mark, firstly after Maya Yoshida deflected the ball onto his own post under pressure from Steven Sidwell and then Paulo Gazzaniga pulled off an excellent stop to deny Hugo Rodallega from point-blank range.
They didn't have to wait too much longer to find an equaliser though and, in the 69th minute, after spreading the ball around the pitch, the ball found Riise on the edge of the box, who drove a vicious effort towards goal only to see substitute Hooiveld deflect it right into the top left corner on the stretch.
The visitors were sensing blood and they went ahead in the 87th minute through Richardson, on as a substitute, after seeing his effort deflected home past Gazzaniga after a some great work by Reither down the right touchline.
The drama wasn't finished there, however, after Fonte nodded in his second of the afternoon at the back post in the 90th minute after getting the better of Brede Hangeland in the air from yet another superb Lallana free-kick.
Despite the hosts piling the pressure on with a swathe of hopeful punts into the box, Fulham managed to hold on and both sides shared the spoils at the final whistle during what was an even and exciting contest.