The Manchester City right-back has been struggling with a groin injury since the UEFA Champions League defeat to Monaco last week, but played 25 minutes as a substitute in Monday's (AEDT) 1-1 home Premier League draw with Liverpool.
The 34 year-old travelled to France's base in Clairefontaine despite being seen limping after the Liverpool match.
He told reporters after the match he would undergo a scan on his arrival and, after tests were carried out, Sagna was withdrawn from the squad and replaced by Lyon full-back Jallet.
France travels to Luxembourg in FIFA World Cup qualifying on Sunday before hosting Spain in a high-profile friendly next Wednesday.
In Sagna's absence, Jallet will compete with Monaco's Djibril Sidibe for selection at right-back.
France has already lost Manchester United midfielder Paul Pogba from its initial squad for the double-header through injury, with Tiemoue Bakayoko replacing him.