The acquittal was read at the Criminal Court in Ratchadaphisek Road in Bangkok today.
The public prosecutor had pressed many charges against him including illegal assembly and rebellion.
He had been accused of taking part in bombing attacks in three southern border provinces including a train station and plotting separation from Thailand.
The court gave the benefit of the doubt to Mr Mahamasakri because the prosecution lacked eyewitnesses to prove the man's wrongdoing.
However, the court prolonged his detention pending an appeal.
Mr Mahamasakri was arrested on September 21, 2012, when he worked as a security guard at an entertainment venue in Phuket.