The Blues had not performed at their best, but they still looked good value for a vital victory at the Madejski Stadium following goals from Frank Lampard and Juan Mata.
Le Fondre had other ideas, though. The striker scored two late goals to give the Royals a 2-1 win at Newcastle two weeks ago and he rescued Reading again tonight, first converting Hope Akpan's pass with three minutes left before taking advantage of poor marking to rifle home.
The Reading fans left the stadium full of joy, but the travelling supporters lambasted their side as they left the pitch.
Stung by an embarrassing draw at Brentford on Sunday, this was a perfect chance to restore some pride and open up a six-point gap over Tottenham, but woeful marking and a lack of creativity at the other end let the Londoners down badly.
The fans who watched Chelsea stutter to a poor stalemate at Griffin Park saw little in the opening half that suggested today was going to be a different story for their team.
Reading winger Jimmy Kebe broke down the right and clipped a ball over the stranded Ross Turnbull, but there was no one on the end of it to tap in.
Chelsea had a large chunk of the possession, but they were sloppy in possession at times and Adam Federici remained untested in the Reading goal.
Some compact defending from Reading meant the away side's only attempt in the opening 15 minutes was an Ashley Cole drive which cleared the bar by 10 metres.
Anti-Benitez chants rained down on Benitez from the away end. "You're not welcome here," the Chelsea fans sang after their customary chanting of Roberto Di Matteo's name after 16 minutes.
Benitez remained unmoved at the edge of his technical area. His team could have had a penalty moments later when the ball appeared to strike Mikele Leigertwood's arm inside the box, but referee Mark Halsey waved play on.
Gary Cahill wasted a glorious chance to open the scoring when he found space in between four defenders in the box, but his free diving header from Lampard's cross flew wide.
Ryan Bertrand found space, but shot well wide. His attempt looked exemplary in comparison to one that followed soon after by Torres, whose shot went out for a throw in.
The Reading fans mocked the Spaniard - but he stunned them into silence in stoppage time, lifting a delicate chip to compatriot Mata, who lost Alex Pearce and beat Federici from five yards.
Chelsea began the second period much better than how they did the first. Lampard chipped a delightful 20-yard pass over the Reading defence for Oscar, but he could only steer his acrobatic effort wide.
Lampard was in the thick of the action again soon after, finding Oscar, who squared for Torres - but Ian Harte cut the Brazilian's pass out just before the £50million man could pull the trigger.
The England midfielder got the goal his performance deserved after 65 minutes when he peeled away from his marker to head Mata's corner in to the far corner.
The Chelsea fans who had barracked Benitez earlier in the match found their voice again to demand their captain for the night be awarded a new contract.
Brian McDermott acquiesced to the Reading fans' demands for the introduction of Le Fondre, but he took until the 85th minute to make an impact, curling a shot that just cleared Turnbull's goal.
The former Rotherham striker was more clinical with four minutes left, however, latching on to Akpan's pass at the back post before beating Turnbull.
Reading threw everything forward and they got their reward when Akpan nodded the ball to the back post. There Le Fondre, one of three unmarked Reading players, calmly converted, to delight the home fans.
The Royals held on for the remaining 30 seconds and secured a vital point that was followed by the playing of 'The Great Escape' over the PA system.