The accused, identified as S. Vetriselvan (35) and N. Mohanraj(28), were arrested on Thursday and sent to judicial custody.
The victim complained that the the accused barged into her room at midnight while she was alone and raped her. She went on a long leave after this incident and rejoined service in October.
The Flower Bazar police registered a case against the accused on Wednesday after the victim filed a complaint before the Chennai City Police Commissioner.
Station House Officer at the Flower Bazar police station told IANS: "After receiving the complaint, we viewed the CCTV footage of the hotel room and found that the two doctors had barged into the room where the woman doctor was staying."
Further investigation is on.