The federation announced the positive tests Wednesday and said the players were partners, but did not name them.
"Since the start of the tournament, 2,446 tests have been carried out to date on the populations of players and their entourage," the federation said in a statement.
"This is the first time this year that the tournament management has had to remove players."
Top-seeded Croatians Mate Pavic and Nikola Mektic were pulled from the field Wednesday and replaced by alternates. Pavic and Mektic were not in the singles draw.
Spaniards Feliciano Lopez and Jaume Munar also disappeared from the doubles draw.
Munar lost to American Reilly Opelka in a second-round singles match Wednesday in Paris. Lopez lost his first-round match Tuesday at Roland Garros.