David Alaba has been out since last December due to a serious knee injury, and the Austria international will not be back for the Spanish giants until the latter stages of this year.
Los Blancos are otherwise in excellent shape, with Dani Carvajal available again after missing the first leg last week, which finished 2-2 in Germany, due to a European suspension.
Thibaut Courtois, meanwhile, made his comeback appearance against Cadiz in La Liga on Saturday, with the team's number one goalkeeper now available for selection after such a long period out.
However, the club's head coach Carlo Ancelotti has already confirmed that Andriy Lunin, who has been the number one for much of the season, will start between the sticks against Bayern at Bernabeu.
David Alaba is Real Madrid's only absentee
"We have to try to do our best. It's a semi-final. We're very excited because it's a great opportunity to reach a final. The difficulties will be many, but we're in good shape and very motivated to do well," Ancelotti told reporters during his pre-match press conference.
"As clubs they are similar, they have a great history and a lot of success in the Champions League. We respect each other and that's fair enough. They did better than us in the first leg.
"We're not over-optimistic but we have great enthusiasm. There is awareness of the difficulties we will encounter in the match. There is no over-optimism.
"I am confident because it's Madrid, because of the squad, because of the fans. We think we're on the good side but [Thomas] Tuchel will think he's on the good side. Today we enjoy and tomorrow we worry.
"I don't know what's going to happen, anything can happen, but we're looking forward to a spectacular night."
Andriy Lunin will start in goal for Real Madrid
When asked about the goalkeeping situation for Wednesday's clash, Ancelotti said: "Lunin is going to play. The plan for a player coming back from injury doesn't change for one game. Courtois is fine but he needs time to get to his best. He played an optimal game."
Real Madrid were confirmed as La Liga champions on Saturday, and they will enter this match off the back of a 3-0 success over Cadiz in Spain's top flight.
Ancelotti rung the changes for the clash with Cadiz, but the likes of Jude Bellingham, Vinicius Junior, Federico Valverde, Toni Kroos, Rodrygo, Ferland Mendy, Antonio Rudiger and Aurelien Tchouameni are set to return to the starting side against Bayern.
There is also a big decision to be made in the middle of the defence, with Nacho, Eder Militao and Tchouameni all options to start alongside Rudiger.
Real Madrid squad vs. Bayern: Courtois, Kepa, Lunin; Carvajal, Militao, Nacho, Vazquez, F Garcia, Rudiger, Mendy; Bellingham, Kroos, Modric, Camavinga, Valverde, Tchouameni, Ceballos, Guler; Vinicius, Rodrygo, Joselu, Brahim