Tawde, an ENT specialist who is believed to be a coordinator of the Hindu Janjagruti Samiti (HJS) and a member of Sanatan Sanstha, was arrested from his home at Panvel in Raigad district by the CBI.
He was produced before the Sessions Court which sent him to the custody of the Central Bureau of Investigation for a week.
The CBI has said it has "cyber forensic evidences" against Tawde and he was interrogated for several hours before being placed under arrest around 8.30 p.m. on Friday.
Earlier, the CBI raised Tawde's residences and questioned him at the Sanatan Sanstha ashram at Panvel.
It was the first arrest since the central agency took over the case in May 2014 following the Bombay High Court directives.
A Sanatan Sanstha spokesperson said Tawde was not a member of the HJS and attempts were being made to tarnish the Sanstha's name.
Dabholkar was gunned down by two unidentified motorcycle borne assailants when near the Omkareshwar Bridge close to his Pune home on August 20, 2013.
His family and others claimed that since he promoted rationalism, he was allegedly targeting by rightwing organizations hurt by his campaigns.
Besides Tawde, the CBI is on the lookout for another absconding rightwing activist, Sarang Akolkar, who is also wanted by the National Investigation Agency for his role in a Goa blast of 2009.