The electoral commission said the son of Muammar Gaddafi is being excluded from running because of the legal implications surrounding his bid.
Following Saif's announcement earlier this month to run for Libya's highest political office, military prosecutors had urged the electoral commission not to process his bid, saying he faces allegations of war crimes during the 2011 armed uprising against his father's regime.
Saif is wanted by the International Criminal Court for the killing during the uprising which eventually overthrew his father.
It is not clear whether General Khalifa Hafter, the Libyan warlord controlling the east of the country has been cleared to run for the presidency.
He is wanted in the US where he was charged for a criminal offense.
Among the contenders for the presidency is the only female candidate, 46-year old Leila Khalifa, a women's rights activist.
Sixty aspirants had filed applications with the electoral commission to take part in the December 24 presidential election.