Marcelo, 24, has a broken fifth metatarsal in his right foot, an injury which he suffered in training on Sunday with Brazil, in the Polish town of Wroclaw.
Marcelo played for Brazil in last week's 6-0 destruction of Iraq and was scheduled to continue as left-back in this week's friendly against Japan.
Instead, he has returned to Madrid to be checked by the Real medical staff.
Upon arrival in Madrid, Marcelo said: "I will be back playing soon. Thanks for all the messages of support I have received."
Marcelo joined Real from Brazilian club Fluminense in 2007 and quickly took over at left-back from compatriot Roberto Carlos. His powerful surges down the left have led to him scoring 14 goals in the Spanish Liga.
To make matters worse for Real, Fabio Coentrao - the club's other left-back - pulled a muscle in Portugal's 1-0 defeat in Russia and will be out for around two months.
Coach Jose Mourinho will probably switch Alvaro Arbeloa from right-back to left-back, and move Sergio Ramos from centre-back to right-back.