Boateng did not return for the second half of Saturday's match after injuring his left thigh. Khedira strained a left knee ligament. The Real Madrid midfielder missed six months of the season after surgery on the same knee.
Assistant coach Hansi Flick says both players have been cleared by medical staff.
Germany plays the United States in its last Group G match on Thursday in Recife. A draw would see both teams advance to the knockout stage, but Flick says ''we want to win the group and we'll play to win.''