He will be replaced by Atletico Madrid's defensive midfielder Mario Suarez, a 25-year-old former youth international who earns his first call up.
"Alonso finished (Saturday's) Granada-Real Madrid game with a problem," the RFEF statement said.
"This morning, the player has been in contact with the federation medical services by telephone and he has described his physical condition and how it has evolved from last night.
"Alonso will be checked over by the national team's medical services as is always the case after a player is ruled out after being called up."
The world and European champions play Uruguay in a friendly in Doha on Wednesday.