The Blues lost 3-2 in Moscow but won the two-legged tie 5-4 on aggregate to move through to the semi-finals and Benitez was thrilled with a very proficient job performed by a side missing some key players.
"In the circumstances, with a tough pitch, some players out and lots of young players it's a professional job," he said.
"I'm really pleased with the effort of the players. The second goal we could have done better but they were pushing and pushing.
"We needed an early goal and Fernando (Torres) has scored it. I'm pleased with the effort but disappointed because they were pushing and pushing and we could have done a little bit better in defence.
"But credit the players because we have gone through."
Fernando Torres opened the scoring in the fifth minute before Ivan Marcano levelled for Rubin prior to Victor Moses edging the Blues ahead in the 55th minute. Gokdeniz Karadeniz then equalised on the night for the Russians after the hour-mark before Bibras Natkho made it 3-2 to Rubin who were unable to score the two goals required to send them through to the final four.