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."
Chelsea's shoddy marking made Le Fondre's task easy. The 26-year-old, who now has 12 goals to his name this season, lost his man to convert Hope Akpan's pass for his first strike.
The Blues defence then unbelievably left three players unmarked at the back post in the final minute of stoppage time and Le Fondre made them pay.
Benitez, whose side had to rely on a late Fernando Torres strike to earn a draw at Brentford on Sunday, refused to criticise his defence afterwards, however, and insisted the club is improving under his stewardship
"We all take responsibility. We don't blame anyone: it's for us to analyse why we didn't kill the game off, and to work to stop the mistakes," the Spaniard said.
"We're still in a really good position in the table, but it could have been really better.
"We are improving a lot. We did an exercise with corners and free-kicks yesterday [Tuesday] and it was fine. Today [Wednesday] for 85 minutes it was perfect."
Brian McDermott, in contrast to his shell-shocked opposite number, was a picture of joy as he talked through Le Fondre's late double strike.
"The two finishes from Alfie (Le Fondre)...," the Reading boss said before pausing for breath. "...the second one was ridiculous. It was a top, top-drawer strike, and to do it at that stage of the game..."
Le Fondre has earned the tag of super-sub after scoring six of his goals off the bench.
McDermott insists the striker is happy with his role, although he did hint he may have to start the hitman after his prolific efforts in the Royals' last two league games.
"I speak to Adam as much as I can. It's difficult for me to pick a team," McDermott said.
"I do the best I can to try and get the right team to get the result.
"He's just a great bloke - that's it. He's funny, has real good banter. He trains like he wants to be the best player in training.
"Of course I'd start with him, but I'm trying to find a way to get results.
"The boy's happy, the team's happy, because of those last few results. I'm so pleased for him and them."
McDermott, whose side are now out of the relegation zone, admitted defeat in his battle to sign Blackpool star Thomas Ince.
"Thomas won't be coming here," McDermott said.
"Blackpool are very strong about wanting to keep him. I'd be amazed if Blackpool lose him in this window. My gut feeling is they've managed to keep him."