The Chelsea-bound midfielder has been struggling to recover and coach Jurgen Klinsmann has decided to rest him in the interests of the longer term campaign.
"It seems that Michael Ballack can not play against Costa Rica," Klinsmann told the waiting press.
"He only trained for 30 minutes on Wednesday and then had to pull out.
"We wanted Ballack on board as he is our captain and leader but it is important that he recovers."
The Los Angeles-based Klinsmann will now decide on his replacement with it likely to come from the duo of Werder Bremen midfielder Tim Borowski or Borussia Dortmund's Sebastian Kehl, but he is hopeful of having his star player back for the second group match against Poland on June 14 in Hamburg.
"We want him to get back to full fitness so that he can be fit for the other games in the competition," he added.