Le Fondre came on to replace the ineffectual Jobi McAnuff for the final 20 minutes of the match with the hosts trailing 2-0 on goals from Juan Mata and Frank Lampard.
Brian McDermott's change didn't look like it was going to have much of an impact as the game drew to a conclusion, but in the 87th minute, Le Fondre showed quick and clever movement to spin behind the Blues defence and fire Hope Akpan's pass beyond Ross Turnbull.
Even that seemed in vain until deep into the fourth minute of stoppage time when Le Fondre was again on hand to volley home a loose ball nodded down from a long free kick.
It was the second game in a row the Royals have staged a comeback from a two-goal deficit following their recovery to beat West Brom 3-2 at the Madejski Stadium three weeks ago.
The draw lifts Reading above Aston Villa and out of the relegation zone on goal difference while also further increasing the pressure on Chelsea's under-fire gaffer Rafa Benitez.
The Londoners looked to be cruising toward only their second win in six in all competitions, but a combination of poor finishing and brittle defending cost them dearly.
The opening period was a dour affair with Chelsea dominating possession but doing little with it until the cusp of the break when Fernando Torres' clever through ball allowed Mata to clip past Adam Federici.
Rafael Benitez: 'It is diffcult to explain because we controllled the game for 85 mins but we made too many mistakes at the end.' #CFC— Chelsea FC (@chelseafc) January 30, 2013
The visitors were buoyed by that opener and came out after the restart looking confident and composed.
Oscar should have doubled the advantage from Lampard's glorious through ball, but he acrobatically volleyed over with Torres waiting for a tap in.
Lampard again released the young Brazilian after 65 minutes, and this time Oscar found Torres unmarked in the box, only for Reading to scramble clear.
Their relief was short lived. From the resulting corner, Lampard rose to thump home Mata's delivery. It looked like all three points would be sent back to the capital.
Oscar wasted yet another chance to secure the points when put clear from Yossi Benayoun's ball as Le Fondre made Chelsea regret their profligacy in front of goal.
Rafa Benitez will no doubt spin out the platitudes that Chelsea were the better team throughout and deserved the victory, but his side lacked the killer instincts and defensive fortitude to secure the result. Nothing Benitez will say will be able to mask that reality in the eyes of the Blues faithful.