"Defender Eder Militao complained of muscle pain in his right thigh after training on Wednesday and after medical exams carried out on Thursday, it was identified a small muscle injury in his right thigh," CBF said in a statement.
"The player has been ruled out of Brazil's next two qualifying matches and CBF expresses its solidarity with the player at this time and wishes him a speedy recovery."
Militao, who missed most of last season due to a torn ACL, is the latest Real Madrid player to suffer injury problems at the start of the season.
Midfielder Aurelien Tchouameni and left-back Ferland Mendy left France's camp ahead of their Nations League clashes against Italy and Belgium due to injuries sustained in Real's 2-0 win over Real Betis on Sunday.
Midfielders Eduardo Camavinga, Dani Ceballos and Jude Bellingham also suffered injuries in the last few weeks and defender David Alaba is still recovering from an ACL tear suffered last season.