Patrick Bamford, who scored his 13th goal of the league campaign, Stuart Dallas and Raphinha all tallied after half-time for Leeds.
Southampton had a chance to be 2-0 up inside eight minutes, but Jannik Vestergaard sent his header wide of the post before Nathan Tella fired straight at Illan Meslier.
Tella, meanwhile, had a penalty overturned by Video Assistant Referee after it was adjudicated he went down own his own in the box.
Southampton, who once had everyone looking up at them in the league table, are now just eight points out of the relegation zone with 13 matches left to played.
Saints are already missing key and may have added another injury to their growing list with Oriol Romeu exiting the match in the 70th minute.
Leeds (3-3-3-1): Meslier; Struijk, Cooper, Llorente; Dallas, Klich (Alioski 59), Ayling; Raphinha, Roberts, (Hernandez 74) Harrison (Costa 46); Bamford
Unused subs: Casilla, Jenkins, Gelhardt, Casey, Cresswell, Huggins
Goals: Bamford (47), Stuart Dallas (78), Raphinha (84)
Bookings: Raphinha (85)
Southampton (4-4-2): McCarthy; Bertrand, Salisu, Vestergaard, Bednarek; Tella (Minamino 58), Romeu (Djenepo 70), Ward-Prowse, Armstrong; Redmond (Ings 58), Adams
Unused subs: Forster (GK), Stephens, N’Lundulu, Ramsay, Jankewitz, Chauke
Bookings: Vestagaard (26), Djenepo (83)