Marcelo was training with the Selecao in Poland on Sunday ahead of a midweek friendly against Japan when he limped off with the foot injury after appearing to twist his ankle in the ground.
Brazilian journalist Fernando Duarte tweeted: "Real Madrid's Marcelo will be out of action for three months thanks to a broken metatarsal in his right foot. Bad news for both club and country."
Spanish newspaper AS also reported that Marcelo was unable to put any weight on his foot as he left the training ground.
Mourinho could also be without another international full-back for next week's match against Celta Vigo after Fabio Coentrao suffered an abductor problem playing for Portugal against Russia on Friday.