The 25-year-old is the Bundesliga’s top scorer with 12 goals in 15 games for RB Leipzig.
He appeared to be caught by a challenge from Real Madrid midfielder Eduardo Camavinga.
The France squad are set to fly to Qatar on Wednesday and will face Australia in their first Group D match.
Nkunku is the latest on a list of high-profile absentees for defending champions France, which includes midfielders Paul Pogba and N’Golo Kante and defender Prisnel Kimpembe.
Manchester United defender Raphael Varane is also still recovering from an injury.
A replacement for Nkunku has not yet been named.