Prosecutors said there was "serious or consistent evidence" against France's Loick Jammes, New Zealander Rory Grice and Irishman Denis Coulson.
The trio, who face a maximum sentence of 20 years in jail if they are found guilty, cannot leave France.
Jammes' lawyer said the charges allowed legal teams to "put forward a real defence" of their clients, "respecting the presumption of innocence".
A woman told police she had been drugged and raped in a hotel in Bordeaux following a league match between Bordeaux and Grenoble on March 11.
A lawyer for Coulson denied the allegations, describing the incident as "a night out between consenting adults".
Grenoble had suspended six players but reinstated them, citing a "presumption of innocence".
Three Grenoble players have been charged with gang rape, reports AFP.