The 23-year-old has made a strong start since joining Newcastle this season, scoring in the Premier League and Europe, including Sunday's 2-0 win over Nottingham Forest.
Woltemade is quickly becoming a crowd favourite in Newcastle, after Bayern Munich board member Karl-Heinz Rummenigge had called the club "idiots" for paying more than 60 million euros to VfB Stuttgart for him.
"Nick Woltemade will not be arriving today due to a flu virus," the German team said. It did not say when the forward was planning to join the squad.
Germany host Luxembourg on Friday before travelling to Belfast to face Northern Ireland.
The Germans are in third place on three points, behind Northern Ireland on goal difference. Slovakia are top on six points with Luxembourg bottom on zero.
The top team from the group qualify for the 2026 World Cup to be co-hosted by the United States, Mexico and Canada, while the second-placed team go into the playoffs.