Blues midfielder Juan Mata opened the scoring in first-half injury-time with a fierce strike across Adam Federici.
Frank Lampard’s thumping header from Mata’s corner put third-placed Chelsea firmly in command at the Madejski.
But Le Fondre fired in Hope Akpan’s pass before guiding in a stoppage-time leveller in a dramatic finale.
Reading knew they only needed a point to move above relegation rivals Wigan and Aston Villa out of the bottom three, but seemed set to remain in danger as Chelsea took command.
However, the Royals were rescued once again by Le Fondre, who also came off the bench to score twice in six minutes in their 2-1 win at Newcastle.
The introduction of fellow substitute Akpan, a recent signing from League One side Crawley Town, also proved instrumental as he provided both goals for Le Fondre.
His clever throughball enabled Le Fondre to fire past stand-in Chelsea goalkeeper Ross Turnbull, again replacing the injured Petr Cech, at his near post.
Turnbull had not even been forced into a save before Le Fondre’s first and was left stunned as the ex-Rotherham striker earned Reading an unlikely point in the fifth minute of stoppage time.
Home goalkeeper Federici launched a long free-kick into the Chelsea box and the visiting defence, minus John Terry who was on the bench, failed to cope with the high ball.
It allowed Jimmy Kebe, and then Akpan, to head into the path of Le Fondre, who managed to keep his composure and score his seventh goal in five matches.
Chelsea were left stunned by the double salvo, which will crank up the pressure on Blues boss Rafael Benitez – again the target of jeers from the away supporters.
The visitors were firmly on course to secure their fifth successive top-flight victory on the road and reduce the deficit on second-placed Manchester City to four points.
A dull first-half sparked into life 50 seconds into stoppage-time as Reading were carved open by a slick one-touch move from the visitors.
Ramires, Oscar and Mata combined for Fernando Torres to scoop the ball into the path of fellow Spaniard Mata who swept a low half-volley across Federici into his bottom left-hand corner.
Before Mata’s goal, Chelsea’s only periods of sustained pressure came after mistakes from Reading carelessly handed possession back to Blues.
And another error allowed Lampard to burst forward as Chelsea forced the corner which led to his goal.
It was the England midfielder’s 10th goal of the season and puts him just six goals adrift of Bobby Tambling’s all-time record of 202 goals for the west London club.
Brazilian midfielder Oscar could have added a third when he was released by substitute Yossi Benayoun’s pass, only to be denied by the on-rushing Federici.
And it proved costly as Le Fondre intervened to earn Reading’s seventh point from their last three Premier League games.