Marcello Trotta gave the Bees a deserved first-half lead but Oscar levelled for the Blues after the interval.
Harry Forrester restored the League One side's advantage on 73 minutes only for Fernando Torres to earn the FA Cup holders a replay with a second equaliser seven minutes from time.
Benitez told Chelsea's official website: "In the first half we didn't do what we had to do. We knew it would be difficult but we made too many mistakes in our approach and the way we wanted to play.
"I was very pleased with the reaction of the players in the second half, we showed quality, character and it was much better.
"They were pushing and we knew it could be difficult, but we kept giving the ball away in simple situations which we could have managed better. You have to perform, we didn't start well and they grew into the game.
"In the second half we showed our real level, like we did last week against Arsenal. We have no excuses as to why we didn't play well in the first half, we just didn't do the right things.
"Oscar and Fernando scored great goals, and it was because the team were doing well and we were creating things."
Benitez also praised Brentford's performance and once again stressed the importance of an FA Cup run.
He added: "Brentford did well, we knew they would play with a high tempo and try to press. Our scouts did a good job because we knew everything they could do, but they did it well, so credit to them.
"For us, it's important to do well in every competition. The top four is the priority, but we want to progress in the other competitions. The FA Cup is massive, Chelsea won it last season and we will try to do it again."