Advocate Sanjeev Punalekar and Vikram Bhave, a member of the Sanatan Sanstha which came under investigators' scanner after Dabholkar's killing, were arrested in Mumbai, said an official of the Central Bureau of Investigation.
They will be produced before a Pune court Sunday, he said, adding that preliminary probe has revealed that Punalekar and Bhave had links with the two men who allegedly killed Dabholkar.
Dabholkar, a renowned anti-superstition activist, was shot dead while he was out on a morning walk in Pune on August 20, 2013.
Bhave, a Sanatan Sanstha member, is a convict in the 2008 Gadkari Rangayatan blast case, and currently on bail.
After he was released on bail, Bhave penned a book in Marathi, titled 'Malegaon Sphotamagil Adrushya Haat' (The invisible hand behind the Malegaon blast).
So far, six people, including Sanatan Sanstha member and ENT surgeon Virendrasinh Tawde, Sachin Andure and Sharad Kalaskar have been arrested by the CBI in the Dabholkar case.
The CBI had claimed that Tawde was the "mastermind" of the conspiracy to kill Dabholkar and veteran CPI leader and rationalist Govind Pansare. Pansare was killed in Kolhapur in February 2015.
Andure and Kalaskar were the ones who shot Dabholkar, the CBI has claimed.
The agency had also arrested Rajesh Bangera, Amol Kale and Amit Digvekar in connection with the conspiracy.
Bangera and Kale are also accused in the Gauri Lankesh murder case. Lankesh was shot dead in Bengaluru on September 5, 2017.
The Goa-headquartered Sanatan Sanstha condemned the arrests Saturday.
"The arrest of Sanjeev Punalekar, national Secretary of Hindu Vidhidnya Parishad, and Vikram Bhave, RTI activist of the Parishad, in the Narendra Dabholkar murder case is strongly protested," the Sansta said in a press note.
The arrests, which took place when a "pro-Hindutva government is in power", smacked of a conspiracy, it said.