After review by Grand Mufti Shawqi Allam, the defendants will be sentenced on April 24. They will remain in custody.
Saad struck the bishop three times in the back of the head with a 90 cm (35 inch) steel pipe while Mansour stood guard outside, prosecutors said during the trial.
Saad had long had differences with his superiors, who on one occasion investigated him for breaking monastic rules and traditions, prosecutors said. Trial witnesses had said violations included seeking to buy and sell land.
He was defrocked in August over what church officials called violations of monastic life and then detained. Prosecutors said he tried to commit suicide with poison after he was defrocked.
Judicial sources said Saad had confessed when questioned about the killing.
The second monk, Mansour, had also attempted to commit suicide after the incident, prosecutors said.