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 Alex Pearce saw his header cleared en route to goal after the break.
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 chances 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.
Reading immediately 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 looked sharper in the second period with Robert Snodgrass forcing 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 appetite to hit on the break 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 out, but the former Rotherham man was on hand to knock in Jason Roberts' cross-shot and spark mass delirium amongst the home supporters.
In the late kick-off,
Kevin Nolan capitalised on an unfortunate ricochet to flick the ball past David Button from close range with only seven minutes on the clock following a corner.
The Tykes were the architects of their own downfall as the visitors were afforded far too much time on the ball throughout.
And it was that lack of pressure on the ball that allowed Nicky Maynard the time and space to pick his spot from outside the box following a neat passing move with a little over twenty minutes gone.
The Hammers, in contrast, put the home side under almost constant pressure.
And that intense pressure - this time applied by Maynard - forced Button into a loose clearance, which Mark Noble collected and from an acute angle chipped over a retreating Barnsley defence to give the visitors a three goal advantage at the interval.
Barnsley made more of a fist of the opening exchanges of the second period but if there were any doubts as to the destination of the points they were firmly extinguished when former Barnsley man Ricardo Vaz Te tapped in from close range after a good run and shot from George McCartney.
The scoreline would have had an extra gloss if Maynard had managed to add to his tally, but first the crossbar and then the assistant referee's flag were to deny the former Bristol City man.
It was to matter little however as the Hammers will go into Monday's crunch clash with Birmingham in buoyant mood after a very professional performance.
The first was a strike of some quality, picking up the ball near the halfway line before slaloming past a number of flailing Watford challenges and then toe-poking past Tomasz Kuszczak in the home goal.
The second half was a more keenly fought affair until Kuszczak brought down Thomas Ince with 70 minutes on the clock as the youngster latched on to a Matt Phillips pass.
Dobbie made no mistake from twelve yards to secure all three points.
Charlie Austin with the composed finish following a fortunate break of the ball in the 23rd minute.