The Spain midfielder suffered the injury during the first leg of the semi-final on German soil, leading to him being substituted at the halfway stage of his side's 2-1 win.
Despite training with the squad on Monday, Isco's name does not feature in Zinedine Zidane's squad for the return fixture at the Santiago Bernabeu.
However, Nacho Fernandez - who has missed the past month of action due a thigh problem - is included.
The defender's return would be timely too, considering the reigning European champions are without regular right-back Dani Carvajal due to a hamstring strain.
Having dropped in to defence to cover for Carvajal at the Allianz Arena, winger Lucas Vazquez could once again be asked to fill the role in the Spanish capital.
Elsewhere, Gareth Bale will be hoping to see minutes in European competition after slipping down the pecking order of late.
Cristiano Ronaldo was rested, but Real's 42-goal talisman will be back to lead the hunt for a Champions League final berth in midweek.