Loic Remy appeared to have given Rangers renewed hope in their survival quest with a stunning 85th-minute strike, only for Maloney to drive home a ferocious equaliser from 20 yards just seconds from the final whistle.
It was a spectacular twist to the match and agonising for QPR who had played all but 20 minutes with only 10 men after Bobby Zamora was sent off for a moment of madness.
In attempting to reach a throw in, Zamora kicked Jordi Gomez, striking the Spanish midfielder in the head with his studs and dropping him to the floor.
Gomez received treatment and having consulted assistant Scott Ledger, referee Phil Dowd sent Zamora off.
It was an inexplicable act from the England forward given his side were in control at the time and the 32-year-old will now miss crucial fixtures against Everton, Stoke and Reading - with his side seven points from safety.
The atmosphere drained from what developing into an entertaining relegation showdown, yet after spending some time adjusting to Zamora's absence, they continued in the driving seat of a match they deserved to win.
But just as they appeared to have done enough to secure a critical victory, Maloney struck to leave them seven points adrift of safety.
The draw will be more palatable to Wigan, but they remain in the bottom three on goal difference.
Flashes of promise were evident from QPR in the opening five minutes as a back heal from Zamora was just missed by Remy and Junior Hoilett narrowly to reach a dangerous ball at the far post.
Better was to come from Remy in the ninth minute when the Frenchman struck the left post with a ferocious shot that had beaten keeper Joel Robles.
But the bright start shuddered to a halt in the 21st minute when Zamora was dismissed for his reckless tackle on Gomez.
The England forward complained bitterly at Dowd's decision and Rangers fans repeatedly jeered Gomez thereafter, but Zamora had left the official with little option but to produce his red card.
Dowd endeared himself to the irate home support by awarding two fouls in quick succession and QPR had the visiting defence at panic stations with a goalmouth scramble.
Julio Cesar kept a well-struck long-range effort from James McCarthy at bay while at the other end only a terrific tackle from Emmerson Boyce prevented Remy from connecting with a cross from Jose Bosingwa.
With space to exploit on the right, Remy was released into the box but his final ball was dreadful.
Adel Taarabt was brought off the bench, replacing Hoilett, and his pinpoint delivery to Remy at the far post was headed narrowly wide by the £8million signing from Marseille.
Despite their numerical advantage, Wigan had barely mustered a shot at goal and it was 10-man QPR who were the more dangerous side.
Wigan would have taken the lead in the 78th minute had substitute James McArthur not directed his header straight at Cesar, who was making only his second real save of the game.
The Latics must have raised their hopes when they were awarded a free-kick 30 yards out, but instead it proved their downfall as the ball was stolen by Stephane Mbia.
Mbia dashed 50 yards and released Remy who rifled home his fifth goal since his £8million transfer from Marseille in January from the edge of the area.
However Mbia barged into the back of Maloney 20 yards out and the midfielder picked himself up to curl in the leveller.