At the next hearing, the court will also decide on 70-year-old Musharraf's plea seeking permanent exemption from appearance in the case.
Additional sessions court judge Wajid Ali granted Musharraf exemption for today's hearing.
Following a request by Musharraf's lawyer to grant him permanent exemption, the judge said he would decide the issue on March 15.
Cleric Abdul Rasheed Ghazi was killed when army troops cracked down on the Lal Masjid to flush out militants who were holed up in the pro-Taliban mosque in Islamabad.
At least 100 people, a majority of them extremists, were killed during the operation.