The Blues looked in control of the contest courtesy of goals either side of half time from Juan Mata and Frank Lampard.
If anything, Chelsea were looking more likely to bag a third than the Royals mount a comeback.
However, substitute Adam Le Fondre scored twice in the closing stages to turn the game on its head and snatch an unlikely point.
Benitez was particularly displeased Le Fondre was left unmarked at the back post in injury time to steer home Reading's leveller.
"It's difficult to explain because we had a lot of chances," he told Sky Sports. "We could have killed the game.
"We conceded two late goals. Especially the last one, a free-kick from the middle of the park. It's difficult to explain.
"They have two players at the back post and we didn't have anyone around. It was a big mistake and we paid for that.
"It was 85 minutes and we knew that it could be this kind of situation. We had to keep the ball in the last minute and score the third goal.
"We changed Mata because he was limping. He had a problem with his ankle. (Demba) Ba could hold the ball in the last few minutes.
"Everything was under control, just the last ball and we didn't have a second player on the back post.
"We controlled everything. We were doing a great job as a team. We couldn't win because of this mistake and we couldn't take our chances."