A second-half brace from Ricardo Fuller eased Southampton away from the Championship relegation zone.
Fuller's two goals could prove crucial to the Saints
Glenn Loovens hit the bar in a goalless first half, then on 47 minutes Claus Lundekvam got a rare goal, glancing in a header from Jim Brennan's fine cross.
Cameron Jerome created chaos and headed an equaliser ahead of Darren Purse.
But Fuller scuffed a goal with the aid of a deflection then volleyed in after Jermaine Wright's corner, leaving Purse's late headed goal in vain.
The defeat looks to have dealt a fatal blow to the Bluebirds' play-off ambitions.
Cardiff manager Dave Jones:
"I do not think we did ourselves justice, we should have been better, and one or two of us just did not step up to the challenge.
"On one hand I am criticising my players - but on the other we have had a fantastic season, we have worked our socks off for 40-odd games, and that is a terrific effort for a squad of our size.
"I have injuries all over the pitch, and almost every one of my squad is carrying a knock of some kind.
"I'm not giving up just yet; I have just told the players there are still a lot of points to be won.
"If we chuck in the towel now, the teams above us start losing, and we are not mentally right to take advantage - then we will kick ourselves."
Southampton head coach George Burley:
"It was a massive win for us and pushes us closer to safety."
Southampton: Miller, Baird, Lundekvam, Kenton, Higginbotham, Madsen (Belmadi 78), Wright, Chaplow, Brennan, Rasiak, Fuller (Jones 80).
Subs Not Used: Smith, Dyer, McGoldrick. Booked: Baird.
Goals: Lundekvam 47, Fuller 70, 75.
Cardiff: Alexander, Ardley, Purse, Loovens (Cox 45), Barker, Koumas, Ledley, Scimeca, Cooper (Boland 78), Jerome, Ndumbu-Nsungu (Ferretti 67).
Subs Not Used: Whitley, Weston.
Goals: Jerome 54, Purse 90.
Ref: P Walton (Northamptonshire).