Seven PSG players have tested positive in the last week, including Mbappe’s forward partner Neymar.
The French Football Federation (FFF) said Mbappe returned a negative result before meeting up with the France squad.
Mbappe scored the winning goal in a 1-0 win away at Sweden on Saturday. A statement from the FFF read: “Kylian Mbappé will not participate in France-Croatia, Tuesday evening at 8:45 p.m. at the Stade de France.
“The result of his Covid-19 test, carried out by UEFA on Monday morning, was found to be positive, he was placed away from the group after receiving the results, at the end of training, before regaining his home in the evening. Kylian Mbappe is now the seventh PSG player to test positive for coronavirus after Neymar, Marquinhos, Keylor Navas, Angel Di Maria, Mauro Icardi and Leandro Paredes.
The French domestic season is already underway but PSG are yet to play because of their run to the Champions League final.
Their opening fixture, a trip to newly-promoted Lens, takes place on Thursday, September 10 before a home game against Marseille three days later.