QPR were forced to play for 70 minutes with ten men after Bobby Zamora was sent off for a needless high challenge on Jordi Gomez.
Wigan struggled to break down the ten men and QPR made them pay five minutes from time with a goal of the season contender from Remy.
However, there was a still a sting in the tail with Maloney scoring with a free-kick from the edge of the box deep into injury time to secure a draw for Wigan.
QPR started brightly and were unlucky not to break the deadlock after just nine minutes when Loic Remy struck the woodwork.
Junior Hoilett chested the ball off to Remy on the edge of the box and he fired in a shot which rattled off the post with Joel Robles in the Wigan goal well beaten.
QPR suffered a major blow after 21 minutes when they were reduced to ten men after Zamora was sent off for a dangerous tackle on Wigan midfielder Gomez.
Zamora caught Gomez on the head with his studs and after lengthy consultation with his assistant referee Phil Dowd showed the QPR striker a straight red card.
Wigan tried to make their numerical advantage count and Callum McManaman twice went close with efforts from the edge of the box, with his first attempt curling over the crossbar and his second shot fizzing just wide of the far post.
Julio Cesar was called into the action three minutes before the break when he was forced to tip James McCarthy's long-range shot round the post but QPR managed to keep them at bay up until half-time.
Harry Redknapp introduced Adel Taarabt ten minutes into the second half and he was quickly into the action crossing for Remy to narrowly head wide of the far post just past the hour mark.
Wigan wasted a great chance to go in front 13 minutes from time when Gomez picked out substitute James McArthur unmarked inside the box, but he headed his effort straight at Cesar.
QPR grabbed what could prove to be a crucial goal come the end of the season five minutes from time with a stunning effort from Remy.
Stephane Mbia led a sweeping counter-attack from inside his own half from a Wigan free-kick to tee up Remy to side-foot a brilliant first-time effort into the top corner to send the home fans into raptures.
Maloney had the final word for Wigan when he curled home his free-kick four minutes into injury time to leave QPR deflated.