The newly promoted side struggled to create chances in their first match back in the Premier League and fell behind after 34 minutes as Michael Kightly’s deflected effort was fumbled into the bottom corner by Reading goalkeeper Adam Federici.
With the seconds ticking down and Stoke seemingly headed for all three points, Dean Whitehead brought down lively substitute Gareth McCleary in the area and Le Fondre calmly converted the resulting spot kick after the Stoke midfielder had received his marching orders.
There were few surprises in the Reading line-up with summer signings Chris Gunter, Danny Guthrie and Pavel Pogrebnyak all handed debuts.
Stoke manager Tony Pulis gave Kightly his debut while Robert Huth also started the match after recovering from viral meningitis.
Reading started out like a side with all the forward momentum of their excellent Championship season as they enjoyed the lion’s share of the possession.
While Reading’s centre-back duo of Kaspars Gorkss and Alex Pearce were enjoying a comfortable afternoon, Ryan Shawcross and Huth had rather more to do, with the German, in particular, forced into several blocks and clearances as Reading pressed.
But for all their possession and positive build-up play, Reading could not muster a single shot on target in the first-half, with Gorkss’ header over from an excellent Danny Guthrie corner the closest they would come in the opening 45 minutes.
At the other end Jonathan Walters was beginning to pose a more sustained threat and after he had curled well over after a neat turn on the edge of the area, he glanced a Kightly free-kick inches wide of the far post.
Stoke’s opener came as little surprise although the manner of it will have disappointed Reading boss Brian McDermott.
Kightly pounced on a loose ball in the box before unleashing a shot that deflected off Gorkss. What should have been a routine catch for the goalkeeper turned into a horrible fumble and the ball squeezed into the bottom corner.
Stoke bossed proceedings for long periods of the second-half. While Peter Crouch was largely anonymous, his strike partner Walters was causing the home defence all manner of problems with his hold up play and excellent first touch.
In defence, Shawcross and the outstanding Huth were repelling the Reading front line, although Le Fondre’s persistence kept both on their toes.
He headed a Jobi McAnuff cross over before McCleary was introduced as a substitute in place of Hal Robson-Kanu in the 66th minute. The former Nottingham Forest winger was vibrant from the outset, making a number of threatening runs down the right.
It was his 89th minute dribble into the box that earned Reading a point.
McCeary was closing in on goal after a one-two with Le Fondre when Whitehead, who had already been booked, brought him down. Referee Kevin Friend had no choice but to point to the spot, and Whitehead was sent-off.
Le Fondre’s penalty was calmness personified as Reading’s late rally was rewarded with a point.