Umarji, 65, who was bed-ridden since his acquittal in February 2011, passed away on Sunday night.
He was suffering from diabetes and depression, said his son Saeed Umarji.
The Maulvi was acquitted along with 62 others by a special court in Ahmedabad after spending eight years in Sabarmati Central Jail, as an undertrial.
On February 27, 2002, a violent mob attacked Sabarmati Express train at Godhra station resulting in the death of 59 people, mostly karsevaks who were returning from Ayodhya. This triggered communal violence across Gujarat and claimed lives of over 1200 people.