At the RCDE Stadium in Barcelona, the home ground of LaLiga club Espanyol, Spain supporters chanted "who doesn't jump is a Muslim" during the World Cup warm-up match, which ended in a goalless draw.
"FIFA has opened disciplinary proceedings today against the Spanish FA for the incidents in the friendly against Egypt," FIFA said in a statement.
Spanish police launched an investigation into the chants last week.
Spain winger Lamine Yamal condemned the chants as disrespectful and intolerable in an Instagram post.
The Egyptian Football Association also condemned the chants as an entirely unacceptable "repugnant act of racism," and added that the acts of a small group of spectators would not affect the close relations between the Spanish and Egyptian federations.