PSG will be attempting to overturn a 3-1 deficit from the first leg, after the two-time defending champions stunned the French side with two late goals at Santiago Bernabeu.
Kroos has not played since that game due to a knee injury, while Modric was sidelined shortly after with a hamstring issue.
Marcelo has been passed fit to start for the Blancos, after the Brazilian left-back returned from a hamstring injury off the bench against Getafe on Saturday.
Modric and Kroos are joined on the bench by Gareth Bale and Isco, with Marco Asensio and Lucas Vazquez prefered in wide areas by Zinedine Zidane.
Injured against Marseille last week, Mbappe passed a late fitness test to make the starting XI at Parc des Princes.
With Neymar sidelined due to an ankle injury, Angel Di Maria steps into PSG's line up in his place, with Presnel Kimpembe and Giovani Lo Celso also making way from the first leg in favour of Thiago Silva and Thiago Motta.
PSG XI: Areola; Dani Alves, Marquinhos, Thiago Silva, Berchiche; Verratti, Motta, Rabiot; Mbappe, Cavani, Di Maria
Subs: Trapp, Kimpembe, Meunier, Diarra, Lo Celso, Draxler, Pastore
Real Madrid XI: Navas; Carvajal, Ramos, Varane, Marcelo; Vazquez, Casemiro, Kovacic, Asensio; Benzema, Ronaldo
Subs: Casilla, Nacho, Bale, Kroos, Modric, Hernandez, Isco