On Tuesday, the north Tripoli court cleared Gaddafi of charges related to the murder of former Libyan star football player and coach Bashir Rayani, the ministry said in a statement.
Rayani disappeared in March 2005 soon after he publicly criticized Saadi. His dead body was later found on the beach in Tripoli near a resort owned by Saadi.
Gaddafi, who under his father was captain of Libya's national football team, has been held in the capital city of Tripoli since his extradition from Niger in 2014. He fled to Niger during the uprising in Libya in which his father was overthrown and killed.
He remains in jail and still faces other charges relating to issuing orders for a crackdown on the 2011 revolution.
One of Rayani's children told local media he would appeal the ruling, adding that his family wasn't allowed to attend the ruling pronouncement, which was not recorded.
Fact: Muammar Gaddafi's son Saadi has played in Serie A for four years (Perugia & Udinese), in which he made just two appearances as a sub. pic.twitter.com/waqkADggpf— Photos of Football (@photosofootball) 26 сентября 2017 г.
"I think it is shocking that Al-Saadi was found not guilty in my father's murder despite the fact that all fingers point at him," Rayani's son said, as reported by the Libya Observer.
"My family and I won't be silent, no matter how long injustice lasts in this country," he wrote on his Facebook page.
The death sentence was previously issued against another of Gaddafi's sons, Saif al-Islam, who was held captive for years in the western town of Zintan. His current whereabouts are unclear.