The 29-year-old Barcelona player has a long list of injury problems, which has restricted his international appearances.
He missed September’s opening four matches at the start of the new Nations League campaign but returned for Friday’s home clash against Greece in Amsterdam.
De Jong was named captain, replacing the injured Virgil van Dijk, but substituted at half-time of the 7-0 victory, saying he had back pain and did not want to take unnecessary risks.
Netherlands coach Xavi Hernandez will not call up a replacement for De Jong, meaning the squad for Berlin will consist of 23 players, the Dutch FA added.
The Netherlands, with 11 points, top Group A2 ahead of Greece and Germany (eight points each). The top two teams advance to the quarter-finals in March.
