Newcastle had looked comfortable at the break after Yohan Cabaye, on his first start since November, had curled home a wonderful free-kick ten minutes before the break, but Le Fondre struck twice in the space of six minutes to earn Reading the points.
If ever there was a must-win game, this was it for Newcastle after a run of just two wins in 13 Premier League games which had seen them slide inexorably towards the scramble for top-flight survival.
Promoted Reading arrived on Tyneside as one of only four sides with a worse record than the Magpies, and they showed glimpses early on and should have gone ahead through Pavel Pogrebnyak as he slid the ball wide.
But it was Adam Federici who kept Reading in the game in the opening 45 minutes after a string of fine saves.
He kept out Papiss Cisse on two occasions with excellent stops, whilst he also saved well from Cabaye before the Frenchman curled home his effort from 22 yards.
The second half saw Reading come out strong, but they could not find a way through and Newcastle looked to have weathered the storm from both the visitors and the conditions as the snow came down.
Then Reading boss Brian McDermott brought on Le Fondre and, within 60 seconds he had levelled. Mikele Leigertwood found Jimmy Kebe with a wonderful cross-field pass, the winger fired the ball into the six-yard box and Le Fondre bundled the ball over the line.
Moments later the home fans were less than happy as Cabaye was brought off, and their mood was somewhat worse minutes later as Reading snatched the lead.
Again Kebe was involved as he nodded the ball down for Hope Akpan, his mis-hit shot fell into Le Fondre's path and he curled the ball into the corner from 12-yards.
Cisse fired wastefully over the top and substitute Gabriel Obertan forced Federici to make a late save in a desperate flurry, but there was no way back for a beleaguered Newcastle.
The win means Reading now move out of the bottom three and to within two points of Newcastle who are firmly in the relegation dog-fight.