Midfielder Xabi Alonso, who has stamped his authority on the side since joining from Liverpool three years ago, picked up a booking against the Russians that means he is suspended for the nine-times European champions' next match.
Alonso performs much the same role as his Spain team mate Xavi at Barcelona and a significant part of Real's build-up play flows through the 30-year-old Basque, whose tough tackling also makes him adept at breaking up opponents' attacks.
"It is very bad news for us," Emilio Butragueno, a former Real player and now a club director, said on Spanish television.
"Xabi is a key man who plays all our games and he has a significant role in our way of playing."
Mourinho acknowledged Alonso's importance to the team at his post-match news conference but said he has other players he can call on to partner German international Sami Khedira in central midfield.
Esteban Granero and Lassana Diarra have similar profiles to Alonso, while Turkey's Nuri Sahin is itching for a chance to prove himself after coming back from injury.
"Xabi Alonso is a great player and very important for us, but we're not going to cry about it as we're solid in midfield," Mourinho said.
"Granero and Lass can easily play with Khedira and Nuri, whose spirits we're trying to raise," added the Portuguese.
"Alonso will rest and that way he will be able to play all the La Liga games and he will be fit to the end."
Asked about his 50th-minute booking, which he earned when the score was 1-0 to Real, Alonso told reporters:
"When it happened on the pitch I had my doubts but I would have to see it again.
"It's a shame but the game was still open and I took a risk," he added. "I knew the situation but at the same time there is no need to turn it into a drama."
Real will learn on Friday who they will face in the last eight, with holders Barcelona, who knocked them out in the semi-finals last season, lurking in the draw along with fellow heavyweights AC Milan, Bayern Munich and Chelsea.
Olympique Marseille, Benfica and APOEL Nicosia are also through, with the first legs to be played on March 27/28 and the second legs on April 3/4.
"The important thing is to be in the quarters and now we'll wait to see what happens on Friday," Mourinho said.
