The Manchester United player, who was one of very few to take part in a light session on Monday evening, left the pitch with a thigh problem with team doctor Franck Le Gall and will return to Manchester ahead of France's upcoming matches.
"Paul Pogba is forced to withdraw from France's next two games at the Parc des Princes against Kazakhstan and against Finland in Helsinki," the statement from France's federation read.
He is being replaced in the squad by AS Roma's Jordan Veretout.
France are top of their qualifying Group D with 12 points from six games and victory against Kazakhstan will secure them a place in next year's World Cup finals.
Coach Didier Deschamps, however, warned against complacency as the world champions take on a side who have not won any of their seven group games.
"The important thing is to reach our goal, to qualify for the World Cup. All my energy and our concentration must be on that," Deschamps told a news conference.
"We must not think that we are already qualified because it is only Kazakhstan. We're going into the game with all our determination and strength to win."
France will also travel to Finland next Tuesday.