The Latics held a seven-point advantage over Harry Redknapp's strugglers ahead of kick off but the London club improved steadily following Bobby Zamora's early dismissal to eventually take the lead through Loic Remy with five minutes remaining.
Wigan looked beaten but Maloney stepped up to curl home a sumptuous free-kick beyond Julio Cesar three minutes into time added on at Loftus Road.
Martinez's men remain in the bottom three but have a game in hand on 17th-placed Sunderland, who lost at Chelsea, while QPR's tally of 24 points keeps them in 19th place with six games still to play.
Martinez told Sky Sports 1: "It's a great point because we were 1-0 down and a late goal like that is a point gained, there's no two ways about it.
"But overall we were very poor and I think that's the worst performance we've had this season. We were cagey.
"If anything the sending-off went against us. We are a team that enjoy having the ball and we can open teams up but we made it a hard task.
"The players know that they haven't done things as well as they should have done but that result is very, very important."
Zamora was shown a straight red card for his 21st-minute foul on Jordi Gomez but Martinez feels the decision worked to the Hoops' advantage.
He added: "It was a horrific challenge. I know Bobby Zamora is not a dirty player but Jordi Gomez is very fortunate - he could have been majorly injured. It was the right decision. As much as you don't want to see red cards, that was as much a red card as you are going to see."
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- Bobby Zamora
- Harry Redknapp