Additional Commissioner of Police S Solunke said Manish Nagori and Vikas Khandelwal were arrested. They were reportedly engaged in illegal sale of firearms.
The two accused are already under arrest in connection with other cases in Thane jail and Pune police were expected to seek their transfer remand to produce them in a city court, sources said.
Police refused to more details about the arrests except confirming it.
The two had earlier been interrogated by Pune Police in connection with the supply of the weapon used to murder a watchman of Pune university some months ago.
Dabholkar, who was in the forefront of anti-superstition movement in the state, was shot dead by two motorcycle-borne unidentified assailants on August 20, when he was out for a morning walk on the Omkareshwar temple bridge in the city. Four shots were fired at him from close range by the attackers.