The Blues looked set to extend their lead over fourth-placed Tottenham to six points after Juan Mata and Frank Lampard struck either side of half-time.
Le Fondre had other ideas, however. The former Rotherham striker came on with little over 20 minutes left and yet again made a crucial impact, beating Ross Turnbull first in the 87th minute and then 50 seconds from the end of stoppage time to hand Reading a vital point.
It was the third consecutive Barclays Premier League game in which Le Fondre had come off the bench to score late on.
"It's difficult how to explain how we drew this game," the Chelsea manager said.
"We were controlling the game for 85 minutes, and even when they started playing long balls in the last 10 minutes we were still in control.
"We can say that we have to be more clinical, and be better at defending set-pieces, but we've been doing a professional, perfect job for 85 minutes. They had their first shot after 78 minutes.
"Everybody had the same feeling. Everyone could see the game was under control for us until the last minute."