The pair are now self-isolating for 14 days, giving them little time to prepare for the new Premier League season, although Ndombele is believed to have tested positive a few days ago.
"I had to make a last-minute change to this list because Paul Pogba was planned to be in this list but unfortunately for him, he took a test [for Covid-19] yesterday which turned out to be positive today, so at the last minute he was replaced by Eduardo Camavinga," said France manager Didier Deschamps.
France travel to Sweden on September 5 before hosting Croatia three days later.
Meanwhile, Ndombele’s Tottenham return to league action against Everton on September 12, while Manchester United face Crystal Palace on September 19 after earning an extended break following their Europa League run.