There was a lack of goalmouth action in a dire first half but Wigan took the lead in the 26th minute against the run of play from a corner. The ball was swung in towards the unmarked Gary Caldwell who powered a header past Artur Boruc to give the Latics the advantage.
The first chance of the game had gone to Southampton. Rickie Lambert played a good ball over the top to Gaston Ramirez in acres of space and he had the time to take a touch but blazed over the bar.
Franco Di Santo forced Boruc into a fine save early on, while the Saints came close to levelling when Morgan Schneiderlin blocked a clearance from James McCarthy, but Ali Al-Habsi made a smart stop.
Southampton ended the first half in the ascendancy but were unable to really test Al-Habsi.
The visitors continued to dominate after the break and levelled in the 64th minute, Jack Cork crossing for Lambert to bravely head home.
They pressed for a winner and struck again with five minutes to go, breaking from a Wigan corner. Substitute James Ward-Prowse ran 50 yards with the ball and found Jay Rodriguez, who in turn slid the ball through to Schneiderlin to sidefoot home.
Wigan seemed down and out but rescued a point right at the death, Maloney sweeping home a Paul Scharner knockdown. However, they remain in the bottom three, still two points from safety.