Kroos' absence was one of two main talking points thrown up by the announcement, with the other being the return of Marco Asensio to the squad after injury.
Dani Carvajal misses the game through suspension, whilst Gareth Bale remains sidelined after aggravating a calf problem on his comeback from injury against Fuenlabrada in the Copa del Rey.
Meanwhile, Zidane has opted to leave Kroos, Jesus Vallejo and Achraf Hakimi out of the squad.
Real's official squad list is as follows: Keylor Navas, Kiko Casilla, Sergio Ramos, Raphael Varane, Nacho, Marcelo, Theo Hernandez, Luka Modric, Casemiro, Marcos Llorente, Marco Asensio, Isco, Mateo Kovacic, Dani Ceballos, Cristiano Ronaldo, Karim Benzema, Lucas Vázquez, Borja Mayoral.
Estos son los 18 convocados para el partido ante el @BVB#RMUCL | #HalaMadrid pic.twitter.com/xYL75SWDN9
— Real Madrid C.F. (@realmadrid) 6 December 2017
Asensio will no doubt be champing at the bit to make an impact on his return following his spell on the sidelines.
'Marca' reports that Zidane sat down with the youngster during his injury and told him how important he is to his future plans.
Asensio has yet to find the net in the Champions League and will be eager to do so tonight, though it remains to be seen if Zidane will throw him in from the start against Dortmund.