The court had granted bail to Vikram Bhave in May, but had directed him not to leave Pune city where the case is being tried.
Bhave was accused of helping two other accused - Sachin Andure and Sharad Kalaskar - who allegedly shot Dabholkar on August 20, 2013 in Pune, with a recce of the spot and escape route.
Claiming that there was a link between the accused in the two cases, the CBI on Friday took the custody of Rajesh Bangera and Amit Digvekar from the Karnataka Special Investigation Team.
Dabholkar’s daughter Mukta, rationalist Shyam Manav and former Maharashtra finance minister Ajit Pawar, among others, were on the hit list of suspected Right-wing Hindu activists.
According to a police officer, Sachin Andure, who had his face covered was taken to the Omkareshwar Bridge, where Dabholkar was shot dead by two motorcycle-borne assailants on August 20, 2013.
The Pune court today extended till September 1 the police custody of Sachin Andure, one of the alleged shooters who killed Dabholkar.
Additional Sessions Judge Vinod Padalkar rejected CBI's plea, saying the court cannot send Kalaskar in its custody as he is in another agency's remand.
The weapon could have also been used in the murder of other activists like Govind Pansare in February 2015, M M Kalburgi in August 2015, and Gauri Lankesh in September last year, CBI said.
Dabholkar, a Pune-based anti-superstition activist, was shot dead while he was on morning walk in August, 2013. Lankesh was shot dead in front of her residence in Bengaluru in September, 2017.
A khukri, three live rounds and a 7.65-bore pistol were recovered on the basis of leads given by Sachin Prakasrao Andure who was arrested recently by the CBI.
Today is the fifth death anniversary of the rationalist, who was shot dead in Pune on August 20, 2013.
SIT sources said the name of Sachin Andure, a suspect in Dabholkar's murder case, was allegedly found in a diary they seized from Amol Kale, the suspected mastermind behind Gauri Lankesh's murder.
Sachin Prakasrao Andure, who was arrested last evening by the Central Bureau of Investigation (CBI), was remanded today in the CBI custody till August 26.
Sachin Prakasrao Andure, who was arrested last evening by the CBI, was produced before the court of judicial magistrate first class A S Mujumdar.
The arrest of Sachin Prakasrao Andure, a resident of Maharashtra's Aurangabad district, was made late in the evening.