The midfielder will remain in Germany during the international break having been forced off during Schalke's 4-1 Bundesliga win over Augsburg on Saturday.
A decision will be made next week on whether he will be fit to return to club action against Eintracht Braunschweig on October 19.
A statement on Schalke's website confirmed he will undergo "intensive conservative treatment" in order to "improve the state of irritation in the left knee."
Schalke have lost just once in all competitions since Boateng arrived from San Siro, with the former AC Milan man scoring four times since his summer move.
Ghana face Egypt in the first leg of their World Cup play-off round clash on Tuesday, before the return leg on November 14.