Roma centre-back Yanga-Mbiwa played the full 90 minutes in Friday's 1-1 draw with Albania, which saw a second-half Antoine Griezmann goal spare the hosts' blushes following Mergim Mavraj's 40th-minute opener.
But it proved to be a costly match for Yanga-Mbiwa, with a hamstring injury rendering him unavailable for next week's visit of Sweden.
Southampton midfielder Schneiderlin was a late substitute on Friday, but he will also be unable to feature at the Stade Velodrome on Tuesday due to an abductor problem.
A brief statement on the French Football Federation's official website read: "Mapou Yanga-Mbiwa (right hamstring) and Morgan Schneiderlin (right adductor) spent Saturday morning at the hospital in Rennes, radiological examinations confirmed their inability to play in the France-Sweden friendly match next Tuesday in Marseille.
"[Head coach] Didier Deschamps took note of these absences and made the two players available to their clubs."