Special CBI judge M B Gosavi passed the order.
According to CBI, the IPS officer and his subordinate had helped the Gujarat police execute the "fake" encounter killing of Sohrabuddin Sheikh.
The court has so far discharged BJP president Amit Shah, Rajasthan Home Minister Gulabchand Kataria, Rajasthan-based businessman Vimal Patni, former Gujarat police chief P C Pande, Additional Director General of Police Geeta Johri, Gujarat police officer Abhay Chudasama, Yashpal Chudasama and Ajay Patel (both senior office-bearers of Ahmedabad District Co-Operative Bank) from the case.
He was killed in a "fake" encounter with police near Gandhinagar in November 2005 after which his wife disappeared. She too is believed to have been killed.
Tulsiram, an aide of the gangster and eyewitness to the encounter, was allegedly killed by police at Chapri in Banaskantha district of Gujarat in December 2006.
The case was transferred to Mumbai in September 2012 at CBI's request.