The Spaniard said that he was "really pleased" for his compatriot, who has had his fair share of critics since joining the Blues from Liverpool.
"It is good for his confidence but his work-rate was also really good so I am really pleased for him," BBC Sport quotes Benitez as saying.
"He trains really well every day so it was just a question of time. He scored two today and hopefully it will be the same in the next game."
Chelsea take a two-goal lead into the second leg of the quarter-final tie after Victor Moses added to their tally at Stamford Bridge.
Natcho netted an away goal for the Russians from the penalty spot.