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.
An already feisty atmosphere in front of a near full house intensified early on with the dismissal of Thompson for a wild lunge on Jobi McAnuff.
Immediately Reading seized the initiative and the visitors were fortunate to survive a scare in the 20th minute when Harte's vicious cross thumped against keeper Andy Lonergan's left-hand post.
Leeds could easily have been reduced to nine men two minutes later when Danny Pugh's terrible challenge on Jem Karacan went unpunished.
Despite their one-man advantage, the hosts failed to create a chance of any major significance for the remainder of the opening period.
And Leeds accelerated out of the traps in the second, with Robert Snodgrass drawing a good save from Adam Federici.
But Reading responded well and Pearce nodded Harte's set-piece onto the roof of the net after 60 minutes.
Leeds were more than happy to soak up the pressure, and their sponge-like approach to defending almost paid dividends when McCormack's 20-yard effort rebounded to safety off an upright.
McCormack then teed up Snodgrass 12 yards out but Federici produced a good save, before the former Cardiff man's thunderous free-kick brought a fumble out of the Australian stopper.
At the other end, Pearce's goalbound header was cleared off the line while Le Fondre followed up McAnuff's deflected effort to slide home - only for his celebrations to be cut short by an offside flag.
But with seven minutes remaining, Reading finally found a way through.
Jimmy Kebe's deep cross to the back post was met by Hal Robson-Kanu who sent a delicate header back across goal for Le Fondre to chest home.
Two minutes later Le Fondre completed the job. Again the required finish came from less than two yards but the former Rotherham man was on hand to knock in Jason Roberts' cross-shot and spark mass delirium amongst the home supporters.