Sudhakar Chaturvedi and Sudhakar Dwivedi alias Shankaracharya, facing conspiracy charges, were granted bail by NIA Court judge SD Tekale.
Both are accused of attending conspiracy meetings, where the terror attack was planned, along with others. Two key accused in the case, Sadhvi Pragya Singh Thakur and Lt Col Prasad Shrikant Purohit, were granted bail earlier.
The Bombay High Court granted bail to Ms Thakur earlier this year, while Lt Col Purohit was given the relief by the Supreme Court last month.
Six people were killed and nearly 100 others injured when a bomb strapped to a motorcycle exploded in Malegaon town in Nashik district, around 200 km from Mumbai, on September 29, 2008.
Twelve people, including Ms Thakur and Lt Col Purohit, were arrested in connection with the blast.
All the accused were booked under the stringent Maharashtra Control of Organised Crime Act (MCOCA), Unlawful Activities Prevention Act (UAPA), besides under various sections of the Indian Penal Code (IPC).