QPR were seconds from a crucial win in their search for survival before Wigan struck an injury time goal.
Harry Redknapp's team were down to ten men in the first half after Bobby Zamora was sent off for a high tackle on Jordi Gomez.
But it was QPR who took the lead on the counter-attack as Loic Remy hit a first time strike past Joel Robles Blazquez in the Latics goal.
QPR were on course for a vital three points when Shaun Maloney stepped up and curled an unstoppable free-kick past Julio Cesar in the 94th minute.
Wigan remain on the bottom three on goal difference but have a game in hand on 17th place Sunderland, while QPR stay 19th, seven points from safety with just six games to go.