The midfielder had been linked wth a move away from the Allianz Arena throughout the close season as AC Milan made an approach for him while Chelsea and Liverpool have been tipped as potential destinations.
Sanches was an unused substitute in Bayern's opening Bundesliga game of the season last week, but was not even among the players available for Saturday's encounter.
And the club's sporting director Hasan Salihamidzic has suggested it could mark the end of the 20-year-old's short spell in Munich.
"He asked the coach to be allowed to think about his future," he told Sky Sport.
"That's why he is not part of the squad today."
Coach Carlo Ancelotti has already stated that he has "no problem" with the Portugal international leaving this summer.
He started just nine of the 26 games he has played for the club in all competitions.