Martin Jol's side came back from a goal down only to surrender a 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 positions so far this term, the club resorted to type in the second half when Jos Hooiveld turned a stinging strike from John Arne Riise into his own net to bring the scores level.
With the second half becoming much more open than the first, Fulham took the lead for the first time through Kieran Richardson late on in the game after converting Sascha Reither's excellent low cross. 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 its 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 Shneiderlin all starting instead.
Fulham manager Martin Jol made just one change to his team, with Alexander Kacaniklic coming in for Mladen Petric who is ruled out with a calf complaint, while the match came a little too soon for Dimitar Berbatov.
The home side's pressure told just four minutes in when Fonte managed to guide in a deft header into the far post after a corner from Adam Lallana.
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 in quick succession after a series of dangerous set-pieces.
Trying to put a lackluster opening half behind it, Fulham went close to troubling the scorers on the hour mark. 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.
Fulham didn't have to wait too much longer to find an equalizer. In the 69th minute, after spreading the ball around the pitch, Riise drove a vicious effort towards goal only to see substitute Hooiveld deflect it right into the top left corner on the stretch.
The visiting side was sensing blood by this point and 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.
However, the drama wasn't finished there. 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 home side 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 end-to-end contest.
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