The court also sentenced to death by firing squad seven other former Gaddafi regime officials including his former intelligence chief Abdullah al-Senussi and ex-prime minister Baghdadi al-Mahmoudi, on the same charges, said Sadiq al-Sur, chief investigator at the Tripoli state prosecutor's office.
Eight other ex-officials received life sentences and seven were given jail terms of 12 years each, he told a news conference carried by al-Nabaa television. Four were acquitted. All but Saif al-Islam are in judicial custody, Reuters reported.
The verdict on Saif al-Islam was passed in absentia in Tripoli since he has been held for four years by a former rebel group in the Zintan region beyond central government control.
The trial began in April 2014 before fighting between rival factions in Tripoli ripped Libya apart in a power struggle which has produced two governments competing for central authority.
The sentences can be appealed and must be confirmed by Libya's highest court. The International Criminal Court and rights groups say they worry about the fairness and competence of Libya's judicial system, although it won the right in 2013 to try Senussi at home instead of at the ICC in The Hague.