Five other accused in the case have also been acquitted. All were out on bail.
The judgement has been passed by a special court 17 years after the blast killed six people and injured more than hundred.
Special judge AK Lahoti said the prosecution couldn't prove the allegations against the accused.
Justice Lahoti said the prosecution couldn't prove the motorcycle used in the blast belonged to Pragya Thakur.
The accused have been given benefit of doubt by the judge.
The blast took place when an explosive device strapped to a motorcycle went off near a mosque in Malegaon, a town about 200 km from here in north Maharashtra, on September 29, 2008.
The accused were facing charged under Unlawful Activities Prevention (Act) and various sections of Indian Penal Code (IPC).
They were charged with conspiracy, murder, attempt to murder, promoting enmity and voluntarily causing hurt, NDTV.