Sessions judge N M Parmar pronounced the verdict, saying there wasn't enough evidence.
On February 28, 2002, a day after the Godhra train burning incident in which 59 people died, BJP workers at Thara had given a bandh call.
There was violence in the village during which 20 shops on the highway were gutted.
On the same evening, over three dozen houses were damaged and set on fire. No one was killed.
Most of the individuals were accused in both the cases. Three of the accused died during the trial; the others were out on bail.