The 29-year-old defender had been named in Gordon Strachan's squad for Scotland’s opening qualifier at Signal Iduna Park in Dortmund on Sunday.
However, the Ipswich Town man will instead remain with his club side to receive treatment.
Berra, who has 28 Scotland caps to his name, picked up the knock in Ipswich's 1-1 draw at Derby County last Saturday as Mick McCarthy's men continued their slow start to the Championship season.
Strachan had already called up Aberdeen's Mark Reynolds as cover for a clash that will see Scotland face the daunting task of attempting to contain the newly crowned world champions.
Berra's last Scotland cap came in a 1-0 win over Norway last November.
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