Casemiro started on the bench for the first time in this season’s knock-out stage, with Mateo Kovacic coming into a three-man midfield alongside Toni Kroos and Luka Modric.
There was no place again for Gareth Bale at the Santiago Bernabeu as Marco Asensio and Karim Benzema supported Cristiano Ronaldo in attack. Lucaz Vazquez was set to start at right-back in place of the injured Dani Carvajal.
Bayern were missing a number of key players, including Javi Martinez, Jerome Boateng, Arjen Robben, Arturo Vidal and Manuel Neuer.
Corentin Tolisso replaced Martinez in midfield while Niklas Suele was brought into central defence. James Rodriguez, on loan from Real, started against his parent club.
Starting line-ups for the Champions League semi-final, second leg between Real Madrid and Bayern Munich at the Santiago Bernabeu on Tuesday (kick-off 1845 GMT; Real Madrid lead 2-1 from first leg):
Bayern Munich (4-4-1-1)
Sven Ulreich; Joshua Kimmich, Mats Hummels, Niklas Suele, David Alaba; Thomas Mueller (capt), Thiago Alcantara, Corentin Tolisso, Franck Ribery; James Rodriguez, Robert Lewandowski
Coach: Jupp Heynckes (GER)
Real Madrid (4-3-3)
Keylor Navas; Lucas Vazquez, Sergio Ramos (capt), Raphael Varane, Marcelo; Mateo Kovacic, Luka Modric, Toni Kroos; Marco Asensio, Cristiano Ronaldo, Karim Benzema
Coach: Zinedine Zidane (FRA)
Referee: Cuneyt Cakir (TUR)