The German Football Association (DFB) confirmed the Bayern Munich forward’s absence via Twitter on Tuesday.
The former Manchester City winger missed training on Tuesday, Germany’s final training session before the Japan fixture on Wednesday.
The DFB has not given details on the nature of Sane’s injury.
Sane came into the World Cup in good form for Bayern, having scored 10 goals in 19 games in all competitions this season, along with six assists.
The remainder of manager Hansi Flick’s 26-man Germany squad trained on Tuesday and are eligible for selection in the matchday side.