Giles Coke scored the winner after 68 minutes, taking Simon Brown's pass to beat hesitant keeper Paul Smith.
Kenwyne Jones and Dexter Blackstock missed chances for the visitors, with veteran keeper Kevin Pressman defiant.
Saints pressed in the closing stages, but the Stags held on to give caretaker boss Peter Shirtliff a vital victory.
Southampton boss Harry Redknapp:
"In real football like this you are put under pressure.
"Mansfield worked their socks off and some of my players found it difficult.
"It was a poor performance. There were no shining lights out there for us."
Mansfield: Pressman, Peers, Day, Baptiste, Talbot, Jelleyman, McLachlan, Coke, Brown, Barker, Birchall.
Subs Not Used: Uhlenbeek, Buxton, White, Rundle, Littlejohn.
Booked: McLachlan.
Goals: Coke 68.
Southampton: Smith, Cranie, Kenton, Mills, Baird, McCann, Delap, Folly (Walcott 72), Dyer, Jones, Blackstock (McGoldrick 81).
Subs Not Used: McNeil, Tejera, Gillett.
Booked: Kenton.
Att: 3,739
Ref: B Curson (Leicestershire).