Interior Secretary Angelo Reyes confirmed that the dead included Abu Sayyaf commander Ghalib Andang, also known as "Commander Robot," and Alhamser Mantad Limbong, alias "Commander Kosovo" were killed in the attack on the high-security detention complex.
Both had been charged with involvement in the Superferry 14 terrorist bombing in February 2004 which killed 130 people.
The two had snatched weapons from their guards Monday and killed three security men and one inmate before holing up in the third floor of the prison with about 100 hostages.
Reyes said
Earlier report: 4 die in Manila prison riot
The jail at Manila's Camp Bagong Diwa had 469 inmates including both Islamic militants and convicted criminals, but only about 10 inmates linked to the Muslim separatist group, said to be linked to Al Qaeda, were behind the uprising, he said.
Two policemen were wounded in the operation, and National Capital Region Police chief Avelino Razon said his forces controlled all four floors of the prison after the assault, in which tear gas and water cannons were used.