Former Hearts and Wolves defender Berra suffered a knee injury in the Tractor Boys' 1-1 draw at Derby on Saturday and will now miss Scotland's opening qualifier in Dortmund.
Gordon Strachan has already called up Aberdeen's Mark Reynolds as cover after Berra was kept behind by Ipswich's medical team for further treatment following the match at Pride Park.
A statement on Ipswich's website said: "Christophe Berra has been pulled out of the Scotland squad after sustaining a knee injury in Saturday's draw at Derby.
"The 29-year-old defender has remained at the club to receive treatment, including having an injection in his knee to ease the discomfort."
Berra won the last of his 28 caps in the 1-0 win over Norway in Molde last November.
A further setback for Scotland was announced this evening when Hull left-back Andrew Robertson was ruled out of the trip to Dortmund.
The SFA announced Robertson's withdrawal on its social media channels, and later confirmed that the 20-year-old has suffered a calf strain.
Robertson, who moved from Dundee United in the summer, hopes to be back for Hull's next game, after the international break.
He wrote on Twitter: "Gutted to be injured but hopefully back for west ham! Good luck to all the boys."