Sami Khedira (L) and Christoph Kramer. Photo: Getty Images
The Real Madrid midfielder, a target of Arsenal, hurt his calf just ahead of kick-off at the Maracana.
Khedira was excellent in the 7-1 humiliation of Brazil in the semi-final scoring and adding an assist for Joachim Low's team.
Low opted for Christoph Kramer of Borussia Monchengladbach to take his place.