The Scot's moment of magic ensured a share of the spoils after the 10-man hosts thought they had stolen victory thanks to a spectacular Loic Remy strike in the closing stages
Rangers faced an uphill task from an early stage as Bobby Zamora was sent off for a neck-high challenge on Jordi Gomez and the Latics dominated thereafter, with the Spaniard and Callum McManaman going closest before James McArthur missed a glorious opportunity.
Loic Remy's sublime strike with just five minutes left, however, had the home side on the verge of three crucial points but Maloney's late intervention stunned Loftus Road.
Junior Hoilett replaced Adel Taarabt for QPR after their 3-2 defeat to Fulham and, on the other flank, Andros Townsend proved a problem from the outset for Maynor Figueroa with his direct approach.
The on-loan Tottenham winger produced a couple of teasing crosses as the R's sought to gain an early advantage. In an end-to-end affair, though, Wigan were the first to register a meaningful effort, with McManaman testing Julio Cesar with a low shot.
A lovely move from the hosts involving Hoilett and Remy resulted in the latter picking up the ball 25 yards out before unleashing a devastating strike which came cannoning back off the upright with Joel Robles in the Wigan goal stranded.
While QPR had come closest, Wigan were quite happy to dicate possession and with Harry Redknapp's men already chasing shadows, what happened next gave the strugglers an even bigger mountain to climb.
Zamora needlessly clattered into Gomez with a reckless neck-high challenge and, following consultation with his assistant, referee Phil Dowd gave the striker his marching orders.
Townsend was proving the only bright note of the afternoon for Redknapp and following more tricky play, he freed Remy but the Frenchman was ruled to be offside.
The Latics continued to monopolise the ball and began to get into good attacking positions, with Gomez and McManaman both firing in shots from range before the latter screwed just wide following delicate build-up play.
McManaman clearly fancied his chances against Armand Traore and drove another shot just wide after beating the left-back with ease but Rangers were able to hold out until the interval.
Roberto Martinez's men kept up the heat straight from kick-off at the start of the second-half, though, with the home side having to withstand wave after wave of Wigan attacks.
Hoilett, Remy and Townsend were all providing willing runners for QPR but their teammates were struggling to string together a succesion of passes. Redknapp reacted by hauling off Hoilett and throwing on Taarabt as he sought a saviour.
The Moroccan almost made an instant impact as his swerving cross found the head of the alert Remy, but he could only steer his effort just wide of Robles' far post. Townsend, meanwhile, sent a dipping free kick just over before Wigan mustered up an even better chance.
Maloney wriggled away from Nedum Onuoha and sent an inviting centre across for McArthur, who somehow contrived to head straight at the grateful Cesar before QPR struck in dramatic style.
A Wigan free-kick was charged down by Stephane M'Bia, who charged half the length of the pitch before releasing Remy. With his first touch, the striker sumptuously smashed the ball beyond a surprised Robles to give Rangers a crucial lead.
It looked like they would hang on as they held out resolutely but Maloney would have the final laugh. The Scot sent his free kick dipping up and over the wall and into the top corner past a statuesque Cesar to silence the home faithful and seal a crucial point for the Latics.