Real, who have won Champions League three years in a row, will play CSKA in Group G on Tuesday without Welsh forward Gareth Bale and Spanish centre back Sergio Ramos, who were injured in Saturday's goalless draw with Atletico Madrid.
Brazilian full back Marcelo and midfielder Isco are also ruled out.
"We will of course use the resources that we have," Lopetegui said. "We understand that the players who are staying home are quite significant losses for us. But our job to resolve this situation."
Lopetegui added that despite the injuries and a difficult start to the season in La Liga, the team were in a "fantastic psychological state".
"This is the second match. Everything is open," he said. "We are playing away and there is no better motivation than that. The team's motivation is at its maximum."
The holes in Real's line-up don't mean that CSKA will have an easy game, CSKA midfielder Alan Dzagoev said.
"There are always enough players for two teams on these types of clubs," Dzagoev said. "I don't think (the injuries at Real) will make our lives easier."
Real and La Liga's other two top clubs -- Atletico and Barcelona -- have made uncharacteristically poor starts to the season but have not lost ground in the race for the league title.
Lopetegui said the team was in the process of regrouping.
"I see that we are improving, that we are playing better," he said. "We have the resources to improve."
Real are second in La Liga, trailing Barcelona with four wins in seven matches. They lead Group G after an emphatic 3-0 win over AS Roma in their Champions League opener last month.
CSKA, fourth in the Russian Premier League, are third in the group after a 2-2 draw against Viktoria Plzen.
Real and CSKA meet at Moscow's Luzhniki stadium, which hosted the World Cup final in July.
(Reporting by Gabrielle Tétrault-Farber,; Editing by Ed Osmond)
