The 19-year-old was named in Fernando Santos' selection for an international friendly against Gibraltar and a World Cup qualifier against Switzerland, despite a muscle injury.
Bayern announced Sanches has now been withdrawn from the squad and will continue to build up his fitness as he awaits his league debut for the club after being an unused substitute in the 6-0 Bundesliga thrashing of Werder Bremen on Friday.
"Renato is still feeling the injury to his muscle and that prevents him taking part in Portugal's two upcoming matches," said Bayern's club doctor Volker Braun.
Sanches, who signed from Benfica in May, will instead continue his individual sports rehab training in Munich.
Euro 2016 champions Portugal are also without star man Cristiano Ronaldo for their upcoming matches as the Real Madrid forward continues to recover from a knee injury sustained in the 1-0 final victory over France.
It was also confirmed on Monday that goalkeeper Marafona had replaced Anthony Lopes, who is nursing a shoulder injury.
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