Boateng has been nursing unspecified muscle problems, the German football association said in a statement, and would miss the game as a precautionary measure after a discussion with head coach Joachim Loew.
It has not yet been decided if he will play in Tuesday's friendly against France in Cologne.
Midfielder Toni Kroos also missed training on Wednesday, after being sidelined with a stomach virus.
The Germans, who topped their World Cup qualifying group with ten wins out of ten matches, have organised a series of high calibre internationals, including against Spain and Brazil in March, as they prepare for their world title defence in Russia next year.
(Reporting by Karolos Grohmann; Editing by Christian Radnedge)
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