Bokhiria, who is presently the water resources minister in the Narendra Modi's cabinet in Gujarat, was made an accused for the murder of a Congress leader.
The apex court on Thursday set aside the Gujarat high court's order which had dismissed his plea for discharge from the case.
In 2008, a trial court had ordered to make Babubhai a co-accused.
Congress leader Mulu Modhwadia was shot dead at point blank range outside his house in Porbandar on November 16, 2005 and Gujarat police had filed a charge sheet after detaining suspected gangster Bhima Dula and 10 others.
In 2008, a trial court charged Bokhiria with murder and conspiracy after the son of Congress leader blamed the minister of being threat to his father's life. Congress leader's son accused Bokhiria on the basis of a piece found from body which stated that Congress leader feared a threat to his life from Bokhiria.
Bokhiria moved to the Gujarat high court against the charged levied on him but when the court did not grant him relief; he approached the apex court against the order.