The acquitted people belong to Godhra, 160 km away. The two buses were escorted by police vehicles. One bus contained all their belongings, while they sat in the other bus.
The police have been told to personally hand over the released people to their relatives, said an official.
A fast-track court here Tuesday convicted 31 people for hatching a conspiracy to burn the Sabarmati Express train in Godhra in Gujarat in 2002, killing 59 people and sparking one of the bloodiest communal riots in India. It let off 63 people, including a key accused, for lack of evidence.