The striker came off the bench to net twice in the final six minutes of a pulsating and at times ill-tempered clash at the Madejski Stadium as the visitors paid the price for the early sending-off of defender Zac Thompson.
Playing his first match since January 31, the youngster was sent off by referee Darren Drysdale after just 12 minutes, leaving Leeds to absorb wave after wave of Reading attacks.
Ian Harte's teasing cross evaded everyone before striking a post after 20 minutes while, after the break, Alex Pearce saw his header cleared en route to goal.
Leeds had their chances to win it late on, with Ross McCormack and Robert Snodgrass going close without success.
Le Fondre thought he had put his side ahead with eight minutes remaining, only to be denied by an offside flag, but he made the most of his next two sights of goal to fire the Royals to the division's summit.
Blackpool moved level on points with fourth-placed Birmingham following a 2-0 win at Watford.
The Tangerines went ahead in the 25th minute when Stephen Dobbie produced a superb finish when he swept the ball into the bottom left corner of the goal.
Blackpool doubled their lead with Dobbie's second goal of the game, from the penalty spot. Thomas Ince knocked the ball past Tomasz Kuszczak, prompting the Hornets goalkeeper to bring down the Tangerines striker.
Brighton occupy the final play-off place but they had a disappointing afternoon, losing 1-0 at Burnley after Charlie Austin converted Josh McQuoid's right-wing pass in the 23rd minute.