Wigan salvages point against Saints
It looked like it would be a very good day for the Latics when Gary Caldwell headed them into the lead in the 25th minute but Southampton were a constant threat and it was no surprise when Rickie Lambert leveled 64 minutes in.
The visitors then thought they had won it as Morgan Schneiderlin finished off a break five minutes from time but there was a sting in the tail as Maloney prodded in from a corner.
Paul Scharner, who was hugely popular during a four-and-a-half-year spell with the Latics from 2006 to 2010, slotted straight into defense after returning to the DW Stadium on loan from Hamburg.
The Austrian was the club's all-time leading Premier League scorer until being overtaken by Hugo Rodallega, but it was Scharner's center-back partner Caldwell who made the breakthrough in the 25th minute.
The game had been a midfield battle between two of the league's passing sides until Wigan created the first chance 13 minutes in.
Jean Beausejour swung over a great cross from the left and Franco Di Santo did brilliantly to get his toe to it and stab the ball towards the far post but Artur Boruc was equal to it.
Three minutes later Southampton really should have scored as Lambert picked out Gaston Ramirez in acres of space 10 yards out.
With the DW Stadium waiting for an offside flag that never came, Ramirez slashed the ball well over the bar, and replays showed he was clearly onside.
The next opening produced a goal, with Beausejour again the architect. The Chilean's corner picked out the head of Caldwell, who, having engineered space, placed his header perfectly into the bottom corner.
Southampton almost leveled straight away in bizarre fashion when James McCarthy took too long over a clearance and smashed it against Schneiderlin.
The ball spun towards the top corner off the Southampton midfielder but Ali Al Habsi managed to claw it away just in time.
The scoreline was harsh on Saints and they dominated the final stages of the first half but were unable to find an equalizer. They came close twice, first Jos Hooiveld heading just wide before Jay Rodriguez's header was cleared by Caldwell at the far post.
Southampton boss Mauricio Pochettino made a change at the break, Steven Davis replacing Ramirez, who had picked up an injury at the end of the first half in a clash with Roger Espinoza.
The visitors continued to do most of the pressing and with a little over half an hour to go Wigan boss Roberto Martinez opted for a defensive reshuffle.
Jordi Gomez replaced Ronnie Stam, meaning Beausejour dropped back into defense, Maynor Figueroa moved into the center and Scharner to right-back.
They continued to live dangerously, though, and Saints surely would have scored had Schneiderlin managed to connect properly with a cross from Lambert, who was proving a real handful for Wigan.
In the 60th minute, Adam Lallana entered the fray for Saints as he continued to work his way back from a knee injury, and four minutes later they had their equaliser.
Jack Cork crossed and Rodriguez outjumped the Wigan defense to head on for Lambert, who bravely beat Al Habsi to the ball at the back post.
Southampton sensed a vital win was there for the taking and they were inches away from going ahead in the 71st minute as Lallana pounced on a half-blocked effort and smacked his shot against the near post.
Wigan finally quelled the siege on Al Habsi's goal but Southampton were not to be denied and, from a Latics corner, Rodriguez burst away down the left, beat a lunging challenge from substitute Callum McManaman and crossed for Schneiderlin to smash home.
Wigan looked down and out but they refused to be beaten and with the match entering the 90th minute Scharner got his head to a corner and Maloney scuffed the ball over the line.