The stay was ordered by a Bench comprising Justices Tarun Chatterjee and Aftab Alam.
Soharabuddin was killed by the Gujarat police in the fake encounter on November 26, 2006, and after couple of days his wife Kauser Bi was also eliminated.
The apex court in May 2007 had refused to transfer the investigation of the case to the CBI.
However, after the chargesheet was filed, Additional Solicitor General Gopal Subramanium, who is assisting the court as amicus curiae in the matter, accused the Gujarat government of protecting the accused persons.
Senior Gujarat police officers -- D G Vanzara (DIG), Raj Kumar Pandiyan (SP) and Dinesh M N (Rajasthan Cadre IPS officer) are among the main accused in the case.