The Toffees started the game much like the hosts, opening the scoring in the 10th minute when Steven Naismith poked the ball past Adam Federici following a comedy of defensive errors which saw the Royals fail to clear on several occasions.
Prior to that goal Everton's Nikica Jelavic was kicking himself for not having more composure in the box when the ball fell kindly to him, however the unmarked striker lashed an audacious scissor kick well over the bar.
David Moyes' men may also feel hard done by following the final whistle after two penalty claims were waved away in the first half.
The first came when Naismith turned into the area leading to a Kaspars Gorkss late challenge, however Martin Atkinson saw nothing wrong with the Latvian's mis-timed lunge.
Moments later, what appeared a fantastic block to deny Jelavic turned out to be a Sean Morrison handball as the Royals continued to ride their luck going into half-time.
However, Brian McDermott's interval team talk must have done the trick as Reading stepped up a gear and Nicky Shorey fed the hungry Le Fondre for a header of the highest class into Tim Howard's top corner in the 51st minute.
It was an inspired move by McDermott to re-introduce Le Fondre for Noel Hunt, who had to be content with a place on the bench, as the strike proved to be problematic for Everton's back four which was missing skipper Phil Neville.
Hal Robson-Kanu, who started in place of Garath McCleary, was more than a handful for Leighton Baines and it proved to be a feisty battle down Reading's right-hand side throughout.
Jason Roberts and Le Fondre kept combining well with Everton having to call upon Seamus Coleman to come across and nick the ball from the goalscorer's feet in a last-ditch tackle.
Le Fondre's persistence up front finally paid off on 79 minutes when he attempted to chest the ball down in the box and was rashly challenged by Coleman in the back, giving Atkinson little option but to award the penalty. The striker dusted himself off to take the spot-kick and drilled it down the middle of the goal with Howard diving to his left.
Marouane Fellaini could have levelled the game for the visitors just minutes after Reading's second but luck was on the hosts' side once more as the Belgian's header cannoned back off the bar and into Federici's arms, helping Reading to claim a priceless three points and a first win of the season.