Having returned a negative test ahead of joining Didier Deschamps' squad for a series of internationals Dubois took part in a training session ahead of the positive test on Tuesday.
"Leo Dubois was placed in quarantine when the results came back after Tuesday evening's training session," the federation said.
Real Madrid's Ferland Mendy has now been called up to replace the Lyon man.
France play a friendly with Ukraine Wednesday ahead of Nations League games with Portugal in Paris on Sunday and in Croatia on October 14.
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