Payet was a fitness doubt for the final against Atletico Madrid after missing Friday's 3-3 draw at Guingamp but declared himself ready to play the day before the showpiece game in Lyon.
He was crying as he left the pitch in the 32nd minute to be replaced by Maxime Lopez.
The former West Ham United midfielder was a key figure in France's run to the Euro 2016 final, although he has not featured for the national team since a 2-1 win over Belarus on Oct. 10.
The 30-year-old had made a strong bid for a recall by coach Didier Deschamps with an impressive run of form which included inspiring Marseille to the Europa League final, but his injury may have ended his chances of playing in the tournament.
Deschamps is due to make name his squad on Thursday.
(Reporting by Richard Martin, editing by Ed Osmond)
