The Euro 2008 finalists will be without a number of midfielders in this week's match, and Joachim Low has yet to decide whether he will call up any replacements
Kroos is being plagued by a knee injury and was already rested for Bayern Munich's 2-1 Bundesliga win over Bayer Leverkusen at the weekend.
The midfielder was initially hopeful of recovering in time for Friday's match, but has now decided to withdraw from the Germany squad as the injury continues to cause him trouble.
Lars Bender, meanwhile, featured for the full 90 minutes for Leverkusen on Saturday, but picked up a heel injury during the match that keeps him out of the game versus Kazakhstan.
Borussia Dortmund's Sven Bender has been struck by a bout of flu and has withdrawn for the match in Astana, too.
Low has not yet called up any replacements and will make a decision on whether to make any additions later on Monday.
Germany meet Kazakhstan in Astana on Friday, before hosting Miroslav Beranek's men four days later.