The Royals looked set to be taught a harsh lesson in the realities of top-flight football after Adam Federici's humiliating howler gifted Michael Kightly a debut goal.
But new signing Garath McCleary came off the bench to turn the game, winning the penalty that saw Dean Whitehead sent off and sent the Reading fans home happy from what was their first Premier League outing for four years.
It could so easily have been otherwise, though, and Royals boss Brian McDermott will be worried how badly out of their depth his side had looked before McCleary's intervention, his three other debutants all disappointing.
So gushing had Reading been about Stoke in the build-up to the game, it was hard to tell whether they wanted to beat them or be them.
They certainly could not have been handed a more awkward opening fixture against a side notorious for being horrible to play against.
And they were not exactly having fun in the sun in an opening half-hour that must have had some fans pining for the Olympics.
A succession of niggly Stoke fouls ruined what little flow there was and even referee Kevin Friend's patience snapped when he booked Whitehead for tripping Reading new boy Danny Guthrie.
Ian Harte's dead-ball skills did cause a few problems but it took until the 20th minute for the first effort on goal to arrive, John Walters' pot-shot careering over the crossbar.
Both sides seemed to be wilting in the heat and took the opportunity for a drinks break while Stoke goalkeeper Asmir Begovic was treated for a facial injury.
Kaspars Gorkss should have hit the target with a free header from Guthrie's corner and Walters was unlucky to steer his own glancing effort narrowly wide from Kightly's free-kick.
It did not matter as Reading simply gifted Stoke the lead in the 34th minute thanks to some calamitous defending and goalkeeping.
The Royals defence failed to clear a routine straight ball, which fell to Kightly, who was given an age to control and shoot.
His strike took a slight nick off Gorkss but not enough to deceive Federici, who embarrassingly allowed it to slip through his arms.
Gorkss' afternoon got worse when he was booked for bundling over Walters before an under-pressure Le Fondre could not quite get his head on Hal Robson-Kanu's cross on the stroke of half-time.
Kightly would have had a second goal shortly after the restart had Gorkss not thrown himself at Walters' hooked cross from Peter Crouch's knockdown.
Reading should have been given a lifeline on the hour mark when Whitehead was penalised for felling Pogrebnyak in full flight on the edge of the box but Friend opted not to produce a second yellow card, presumably deciding the Stoke midfielder did not have time to get out of the way.
He also waved away two half-hearted Pavel Pogrebnyak penalty appeals, before the home side threw on McCleary for Robson-Kanu.
McCleary instantly provided the guile Reading had been missing with a lovely reverse pass to Pogrebnyak, whose shot was blocked behind for a corner which saw the Russian nod the hosts' first effort on target straight at Begovic after 70 minutes.
That was the striker's final real contribution as the changes continued for both sides but Stoke looked certain to cling on before dramatically falling apart in the 88th minute.
McCleary was allowed to advance unchallenged into the area and was upended by Whitehead.
Friend allowed play to continue and fellow substitute Noel Hunt was denied by Begovic but the referee brought play back, awarding the penalty and showing Whitehead a second yellow card.
Le Fondre despatched the spot-kick to spark pandemonium at the Madejski, which was almost repeated when Robert Huth gave away a stoppage-time free-kick that Harte curled inches over the top.
|Reading||Team Statistics||Stoke City|
|0||1st Half Goals||1|
|2||Shots on Target||3|
|6||Shots off Target||4|
|51.3||1st Half Poss.||48.7|
|55.3||2nd Half Poss.||44.7|