The Portuguese center back, who put the Saints ahead in the fourth minute by shouldering in a left-wing corner, saved them from a sixth loss in seven matches by glancing in Danny Fox's free kick.
Fulham staged a second-half fightback, with Southampton defender Jos Hooiveld diverting a driven cross by John Arne Riise into his own net in the 70th. Hooiveld also deflected Kieran Richardson's goalbound shot past goalkeeper Paulo Gazzaniga to put Fulham 2-1 ahead in the 88th.
Southampton climbed above Reading to fourth from bottom in its first season back in the top division.
Southampton draws 2-2 with Fulham in EPL thriller
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