Gary Cahill of Bolton Wanderers has been called up for the first time in place of the Manchester United centre-back who joins club mate Michael Carrick on the sidelines.
The 23-year-old Cahill, who has been in outstanding form for Bolton, has been a member of the U21 squad.
Ferdinand suffered the injury before playing in last week's Champions League final defeat by Barcelona in Rome, and while it will keep him out of the trip to Almaty he could feature against Andorra in England's next qualifier on Wednesday week.
Ferdinand's injury is the latest setback for manager Fabio Capello who was already without goalkeeper David James, defender Phil Jagielka and forward Aaron Lennon.
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