Adam Bolder's controversial winner lifted QPR off the bottom and extended their unbeaten run to four matches.
Martin Rowlands fired a penalty against the post after Rowan Vine had been tripped by Charlton's Jonathan Fortune.
Mikele Leigertwood missed another golden chance for QPR when he shot wide with just keeper Nicky Weaver to beat.
But Bolder then pounced on the loose ball to score after Weaver seemed to be fouled by Marc Nygaard as he tried to gather Chris Barker's left-wing cross.
"Our movement was too over-indulgent and we needed to be tighter. Take nothing away from QPR, they deserved to win and we put in an inept display.
"We were booed off by our fans and rightly so."
"I'm just told to get on with the job. I've not got involved in the politics.
"I just prepare the team as best as I can. And on today's showing, we've got a great chance of climbing up the table."
Charlton: Weaver, Mills, Sodje, Fortune, Basey, Sam (Racon 85), Zheng, Semedo (Jerome Thomas 46), Reid, Varney, Iwelumo (McLeod 68).
Subs Not Used: Randolph, Bougherra.
Booked: Sam, Reid.
QPR: Camp, Mancienne, Stewart, Cranie, Barker, Rowlands, Leigertwood, Bolder, Ephraim, Nygaard, Vine.
Subs Not Used: Cole, Bignot, Ainsworth, Sahar, Moore.
Goals: Bolder 72.
Att: 23,671
Ref: Lee Probert (Wiltshire).
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