Earlier, Pune police was investigating the high-profile case but there was no headway following which a PIL was filed by former journalist Ketan Tirodkar seeking a CBI probe into the case.
"The PIL is allowed and the case is being transferred to CBI," said Justice P V Hardas.
Dabholkar was shot dead by unknown assailants in Pune on August 20, 2013.
Yesterday, HC had reserved its order on the PIL after CBI lawyer contended that there was no need to transfer the probe to the investigating agency as no allegations had been levelled against the State or police for shoddy investigations.
Tirodkar had pleaded that even if no allegations were made against authorities, the probe in a criminal case could be transferred to CBI if it has national or international ramifications.
He had also cited judgement in the case of NCP leader Padamsinh Patil who is accused in a murder case, saying the probe was transferred to CBI by the court which did not comment about the role of police.
Pune police had earlier submitted case diaries and confidential reports to the court. After going through them, the judges yesterday sought to know the status of the probe, and asked CBI what was its stand.
The government had also informed that so far the main conspirators had not been arrested, and those, who were arrested, had got bail.
Dabholkar's daughter Mukta, who has been allowed to intervene, had said the family wanted the HC to monitor the probe. She had earlier demanded formation of a Special Investigating Team (SIT) as police were not making any progress.
She had said that her family felt the need for precaution against political interference in the investigation.