Blues boss Graham Potter expressed concern over Fofana’s condition following Chelsea’s 2-2 draw with Everton on Saturday, although the centre-back was initially diagnosed with “fatigue”.
Further tests on Sunday confirmed that Fofana had a minor muscle problem.
The 22-year-old now misses the chance to make his debut for France, who will play against the Netherlands and Ireland in the Euro 2024 qualifiers.
Les Bleus also saw Arsenal defender William Saliba withdraw and has called up both Monaco’s Axel Disasi and Nice’s Jean-Clair Todibo as replacements.
Fofana’s Chelsea teammate Benoit Badiashile is part of the Under-21 squad.
Fofana is now in a race to return from the international break as Chelsea face an Aston Villa side who are just one place below them in the Premier League table.
Thiago Silva also remains injured but is expected to return in April, while captain Cesar Azpilicueta is sidelined with a concussion. Their absence could open the door for Trevoh Chalobah to start.