The Frenchman has been selected to lead the Blancos' attack, while the Portuguese teams up with international colleague Cristiano Ronaldo on the left flank as he replaces Marcelo
The trainer has preferred the Frenchman over striker Gonzalo Higuain, with a supporting cast of Cristiano Ronaldo, Mesut Ozil and Angel Di Maria in attacking midfield.
Left-back Marcelo has been dropped, with the trainer choosing his countryman, Fabio Coentrao, to play in defence opposite Alvaro Arbeloa. In the centre of defence, Sergio Ramos and Pepe retain their starting roles.
Mourinho's opposite, Jupp Heynckes, has decided to give Bastian Schweinsteiger a second consecutive start, despite having his doubts on Monday as to whether the vice-captain was fully fit for the clash. The Germany international will partner Luiz Gustavo in defensive midfield.
Toni Kroos has been selected to start behind lone striker Mario Gomez, meaning that Thomas Muller will have to settle for a substitute's role. Arjen Robben and Franck Ribery will play on the flanks.
Kick-off from the Allianz Arena is scheduled for 20.45CET.
Bayern Munich (4-2-3-1): Neuer; Lahm, Boateng, Badstuber, Alaba; Luiz Gustavo, Schweinsteiger; Robben, Kroos, Ribery; Gomez
Subs: Butt, Rafinha, Contento, Pranjic, Tymoshchuk, Olic, Muller
Real Madrid (4-2-3-1): Casillas; Arbeloa, Ramos, Pepe, Coentrao; Khedira, Xabi Alonso; Di Maria, Ozil, Ronaldo; Benzema
Subs: Adan, Marcelo, Albiol, Varane, Kaka, Granero, Higuain