The government had appealed against the life sentence, calling for the death penalty as the nine men had waged war against the Yang di-Pertuan Agong, a crime under Section 121 of the Penal Code.
Court of Appeal judge Mohd Zawawi Salleh, who chaired a three-member bench, announced the unanimous decision against Filipinos Atik Hussin Abu Bakar, Basad H Manuel, Ismail Yasin, Virgilio Nemar Patulada, Salib Akhmad Emali, Al Wazir Osman, Tani Lahaddahi, Julham Rashid and Datu Amir Bahar Hushin Kiram, all of whom are aged between 42 and 77.
The nine had appealed against their life sentence.
On Feb 11, 2013, some 200 Sulu militants entered Sabah waters and landed in Lahad Datu.
After a stand-off for several weeks, Malaysian security forces eventually engaged with the militants.
The incident ended with the death of 56 militant, 10 Malaysian security officers and six civilians.
The surviving militants were caught or surrendered, and the conflict was declared ended on April 10, 2013.