"I'm disappointed how we defended tonight, especially in the second half," the Spaniard told reporters after Chelsea conceded three goals after the break to lose the return leg 3-2 at Moscow's Luzhniki stadium.
"We became a bit careless, maybe too confident after scoring an early goal. We did well in the first half but I was disappointed how we played after the break, not only the defence but the whole team."
Benitez, however, was pleased with his compatriot, Spain striker Torres, who scored three goals over the two legs.
"Fernando played very well, he has done well in the last few games. He is working hard, creating chances for himself and his team mates," the manager said.
Chelsea midfielder Frank Lampard said the referee was wrong to award a penalty from which Rubin scored the winner on the night.
"I just couldn't believe the referee called it. There was nothing there," the England international said about the 75th-minute foul given against defender Cesar Azpilicueta for pushing. "Luckily, we had enough cushion to get through."
Benitez's counterpart, Rubin coach Kurban Berdyev, blamed "childish mistakes" for his team's failure to overturn a 3-1 deficit from the first leg.
"We wanted to be aggressive right from the start but our plan failed because my players made childish mistakes and allowed an early goal by Chelsea," Berdyev told Russian television NTV Plus referring to Torres' fifth-minute opener.
"We were stunned by that goal, it had really knocked us out. It took almost the entire half for us to get back into the game.
"But I'm really pleased with our play in the second half, I'm proud of the way we came back and won the game," he added.
"This is truly a historic win for our team, although I'm disappointed that we couldn't go through."