When the Spain international was withdrawn it was still 1-1 at Craven Cottage, but the Reds capitulated in the closing stages, conceding two goals and having two players sent off.
However, Benitez, who has seen his side lose six of their last seven matches, says Torres cannot play a full 90 minutes as he is struggling with a groin injury.
"It is a big risk if you keep a player playing if he has this problem so we wanted to protect Torres as we knew it could be worse for him," said Benitez.
"If you lose the player for 20 minutes it is better than for one month.
"We knew that we had to change him. In the last game he played 80 minutes and needed four days to recover.
"He was always training with pain. We knew that we had to change him but it was a question of when and we did it at the moment we did. I think that it was best for him."
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On the red cards referee Lee Mason showed to Philipp Degen and Jamie Carragher, Benitez added: "I think the two sending offs were very harsh. The first one could be a yellow card and for the second one Carragher definitely kicked the ball.
"Zamora was also saying he kicked the ball and we have to analyse this because it is a situation that saw us playing with nine players.
"We were in control at 1-1 and I was really surprised we made these mistakes."
- Liverpool Team News