A bench of justices Aftab Alam and R M Lodha stayed the court proceedings in the case in Banda and directed the Uttar Pradesh Police to hand over the investigation to the agency.
The court passed the order on a PIL filed by advocates Raja Ram and Irudaya Nathan seeking an independent probe into the incident, alleging that impartial investigation was not possible in the case as the ruling BSP legislator and his aides were involved.
The state government did not oppose the plea for CBI probe and agreed to hand over the case to the central agency.
The petitioners alleged that the authorities had committed a grave error by foisting false cases against the victim, who was a minor and was entitled to protection under the provisions of the Juvenile Justice Act.
Alleging that the police and judicial officers were trying to protect the MLA, they alleged that the magistrate, in violation of the JJ Act, had sent her to jail while she should have been sent to a juvenile care centre.
The 17-year-old Dalit girl was allegedly raped by Dwivedi in Banda on December 10 and 11 last year. The girl had escaped from his residence on December 12 when the MLA allegedly attempted to rape her again.
The girl, however, was arrested after alleged false charges of theft were levelled by the legislator`s brother against her.
48-year-old Dwivedi, who was later arrested from Banda and suspended by Mayawati`s party, denied all the charges.