The Blues had taken an early lead through Fernando Torres, but the Russian side piled on the pressure in a manic second half to fight back and claim victory on the night, but fell just short of progressing to the semifinals.
Benitez says the defeat is inconsequential because Chelsea managed to reach the last four with a heavily rotated squad but he admitted disappointment over how his side fared in the second half.
"It doesn’t matter too much because of the circumstances like the pitch and people like Paolo [Ferrerira] and [Nathan] Ake playing. It was a professional job even though the second goal was disappointing," he told ESPN.
"I am disappointed a little because they were pushing and pushing but the atmosphere was not easy so credit to the players."
The 52-year-old also insisted he did not pick his team solely with Sunday's FA Cup semifinal against Manchester City in mind but admitted the crucial cup clash did play some part in his thinking.
"This game is not preparation for the next game but we have to manage both. Some players will not play on Sunday but there is competition for places and that is good for the squad," the Spaniard added.
Frank Lampard was reluctant to make excuses after the defeat but felt the artificial surface at the Luzhiniki Stadium hindered the Blues' short passing game.
"It’s a different bounce on the artificial pitch – it’s more spongey. It holds up on short passes a bit. There’s no excuse we did ok on it in the end," the midfielder told ESPN.
While looking ahead to a potential final at the Amsterdam ArenA, Lampard reiterated the importance of taking one game at a time.
"We just need to concentrate on every game now but we have a big squad and today is a confidence boost for us. We want to get to the final now," he added.
"I think when we get out there we are very professional and the closer you get to the final the more special it gets."