The Blues fell behind twice to their lower league opposition but a late Fernando Torres goal salvaged a draw for Benitez's side and took the tie to a replay at Stamford Bridge.
The Spanish manager was less than happy with his team's performance during the first half after Brentford took the lead through Marcello Trotta and acknowledged that they must be better in the return fixture.
"We knew what Brentford were capable of and they did it well, so credit to them, but we need to do our job in the replay," Benitez told reporters.
"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."
Benitez did, however, praise Chelsea's performance in the second half following the introduction of Juan Mata as a substitute.
"I was very pleased with the reaction of the players in the second half, we showed quality, character and it was much better," he added.
"I changed Mata at half-time and he made a big difference. We were controlling the game and I thought I would bring Demba on for the last 10-15 minutes to try to do something.
"We were on top of them, but sometimes it's good if you change things, and Demba did a great job on the left."
Benitez insisted that he is keen to make an attempt to retain the trophy after Chelsea emerged victorious at Wembley last season but admitted that his priority is the Premier League.
The 52-year-old also expressed his frustration at the difficulties presented by a congested fixture list when competing in multiple competitions.
"For us, it's important to do well in every competition," he claimed. "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."It's very difficult; we are playing a game every three days. How can you train the day before? How can you train the day after?
"We have to use the same players all the time, so hopefully the players that are injured will be able to come back, and hopefully the players at the Africa Cup of Nations will be back sooner rather than later.
"The positive was the reaction of the team, but the negative is that we are using some players too often. We are a strong team but we have problems because certain players are playing 90 minutes all the time, it's not easy."