Low, whose future as Germany coach will be decided after the World Cup, will, however, travel to Port Elizabeth with the team for Saturday's match.
Captain Philipp Lahm was also down with the flu while Lukas Podolski, Miroslav Klose and second choice keeper Tim Wiese were also missing from the training session at Atteridgeville near Pretoria, recovering from minor injuries.
Germany lost 1-0 to Spain in their semi-final on Wednesday and will play Uruguay, who were defeated 3-2 by Netherlands.
Germany manager Oliver Bierhoff said it was not yet clear who would play against Uruguay but said the team was determined to help Klose, should he play, level Ronaldo's World Cup goal record of 15. Klose has scored 14 in three tournaments.
"I think there is a big drive within the team and also his wish to move higher up the list. It would also give the team some pride," Bierhoff told reporters.
He said it was also not clear whether Germany would field a full-strength team or if substitutes would start.
"On the one hand we want to win this match and then there is the thought to thank the substitutes, who have been exceptional in training, throughout all this period.
"We want to end this tournament on a high note."
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