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The Saints thought that they had snatched the points with a late goal of their own when Morgan Schneiderlin put them ahead five minutes from time.
However, Maloney scrambled the ball over the line from a corner as Wigan ensured that they would not be the only side in the Premier League's bottom six to lose this afternoon.
Boruc had previously kept the game goalless with a fantastic full-stretch save which foiled Franco Di Santo's guided effort.
The visitors threatened more regularly in the second period and were rewarded when Lambert bravely stooped to nod the ball home under pressure from Ali Al Habsi.
Saints top scorer Lambert could have bagged a second if he had controlled a back-post volley, and later provided Jos Hooiveld with a glorious chance to put them ahead.
The centre-half could not make contact with Lambert's cross, but Schneiderlin did show composure in front of goal when he converted Jay Rodriguez's pass on 85 minutes.
That was not to be the last of the goalscoring action, though, as Maloney poked the ball into the net from close range to prevent Southampton recording their first win under Mauricio Pochettino.