His absence will come as a major blow for the Barvarians as they look to overturn their 2-1 first-leg defeat at the Bernabeu.
Martinez was forced off in that game due to a head injury, but a significant improvement in recent days meant he was expected to line up in midfield in the Spanish capital.
However, having not felt well on Tuesday, the former Athletic Bilbao man has now pulled out at the 11th hour, leaving Jupp Heynckes little time to shuffle his pack.
Frenchman Corentin Tolisso is expected to take his place in midfield.