The five-time European winners failed to reach the knockout phase for the first time under Spanish coach Benitez despite beating Hungary's Debrecen 1-0 on Tuesday.
Fiorentina's victory over Lyon helped the Italian side book a last-16 berth along with their French opponents.
"I like to win every game and be as high as possible in all the competitions but I think more about the players, the staff and the fans and I'm disappointed for everyone," Benitez said on Liverpool's official website.
"To win is always the target but when you are doing as well as you can you just have to think about the next target.
"We cannot win the Champions League, we know that. A lot of teams don't play in the Champions League. So we have to think about Everton and then the Europa League."
Liverpool, who face Everton in the Merseyside derby on Sunday, will now play in the Europa League - the continent's secondary competition.