With Manchester City completing a thumping 4-0 win over West Bromwich Albion at the Etihad Stadium, United's lead at the top was cut to five points after former Celtic forward Maloney skipped to the edge of the visiting box to send a lovely flighted finish beyond David De Gea.
In truth, Sir Alex Ferguson's side got what they deserved from the match having turned in a listless display for much of the night. Defeat ends their eight-match winning sequence and a 12-match unbeaten run, but they must hope this loss does not have a lasting effect on their bid to defend their title.
United and City have five games remaining of the campaign with United still to visit their city neighbours on the penultimate match of the season on Monday April 30 for a contest that could yet decide the destination of this year's flag.
Wigan basked in a wonderful win coming after two poor decisions saw them lose 2-1 at Chelsea on Saturday with both of the home side's goals offside. It was their first victory over United after 13 straight defeats in the Premier League.
They were unfortunate to have a goal disallowed here on 30 minutes when Gary Caldwell was deemed to have fouled De Gea as Victor Moses rose to power a header into the net, but they never let their heads drop as United struggled for any fluency.
To sum up a pretty abject evening for the champions, Wayne Rooney was hauled off on 62 minutes to be replaced by Nani as United struggled without the influence of Paul Scholes, who was rested after scoring and running the show in the 2-0 win over Queens Park Rangers on Sunday.
Rooney was guilty of switching off for the Wigan goal as Maloney worked a quick one-two with Jean Beausejour before leaving De Gea with no chance.
United did little of note with most of the action centred round the visiting goal in both halves as De Gea made notable stops from James McCarthy and Moses while substitute Mohamed Diame should have sealed a 2-0 win when he slid the ball wide on 79 minutes.
Danny Welbeck forced Ali Al Habsi to repel a venomous drive in the closing moments, but otherwise the Wigan keeper had a quiet night.
The Latics's reward for their win sees them move out of the bottom three of the table. They are two points clear of third-bottom Bolton, and level on 31 points with QPR.