The Portuguese pulled up during a training session with a suspected muscle problem and has handed Jose Mourinho an unwelcome selection headache ahead of the Istanbul clash.
Sergio Ramos will not feature in Turkey either thanks to his first-leg yellow card, meaning that Raul Albiol and Raphael Varane will line up alongside each other in the heart of defense.
It remains to be seen how long Mourinho will be without the services of his compatriot but the former Porto defender seems certain to miss the Turk Telekom Arena clash.
"Following the Levante game, we had some injury worries about Pepe, so we'll wait for tomorrow and then see. Albiol may play instead of him," the former Inter coach said at his press conference.
The Spanish champion will also be without Xabi Alonso, who was also booked at the Bernabeu, meaning that Luka Modric is likely to partner either Sami Khedira or Michael Essien in midfield.