The 18-year-old who was injured during Germany’s final training session ahead of their last World Cup warm-up against the United States in Chicago, has been replaced in the squad by RB Leipzig midfielder Assan Ouedraogo.
World Cup regulations allow national teams to make injury replacements up to 24 hours before their opening match in cases of serious injury or illness.
Germany begin their World Cup campaign on June 14 against debutants Curacao.
Karl’s absence is a major setback for Julian Nagelsmann’s side, with the Bayern Munich youngster regarded as one of the brightest emerging talents in world football.
He enjoyed a breakout season at club level and became Bayern’s youngest-ever Champions League goalscorer.
He made his Germany debut in March and featured in three international matches, including a start in last week’s 4-0 win over Finland.