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.
Rangers faced an uphill task from an early stage as Bobby Zamora was sent off for a neck-high challenge on Jordi Gomez in the 21st minute, and the Latics dominated, with Gomez and Callum McManaman going closest before James McArthur missed a glorious opportunity.
It was Rangers who threatened next and came within inches of grabbing a vital lead.
A lovely move from the hosts involving Junior Hoilett and Remy resulted in the latter picking up the ball 25 yards out before unleashing a devastating strike that came cannoning back off the upright with Joel Robles in the Wigan goal stranded.
Andros Townsend then provided another bright note for Harry Redknapp's side, and following more tricky play from the on-loan winger, he freed Remy, but the Frenchman was ruled to be offside.
The Latics then monopolized the ball and began to get into good attacking positions, with Gomez and McManaman both firing in shots at range at Cesar before the latter hit just wide following delicate build-up play.
Roberto Martinez's men kept up the heat on the R's staight from kickoff at the start of the second half, with the home side having to withstand wave after wave of Wigan attacks. Redknapp reacted to QPR's struggles by hauling off Hoilett and throwing on Adel 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 then 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 cross for McArthur, who somehow contrived to head straight at Cesar.
Just when the game appeared to be fizzling out, Rangers struck. And how. A Wigan free kick was charged down by Stephane M'Bia, who charged half the length of the pitch before releasing Remy, who, with his first touch, sumptuously smashed the ball beyond a surprised Robles to give Rangers a crucial lead.
It looked like they would hang on for three precious points, but Maloney had the final laugh. The Scot sent his free kick dipping up and over the wall and into the bottom corner past a statuesque Cesar to silence a hostile R's faithful and seal a point for the Latics.