The original lawsuit was filed by Somalis living in the US under 1991’s Torture Victim Protection Act.
A federal judge had originally ruled that Mr Samantar was entitled to diplomatic immunity.
Mr Samantar currently lives in the US state of Virginia.
The lawsuit accuses Mr Samantar of commanding his troops to detain, torture, and kill members of Somalia’s Isaaq clan.
The justices said that although the Foreign Sovereign Immunities Act of 1976 shields foreign states from being sued in American courts, it does not shield former officials of those states.
Omar Jamal, the first secretary of the Somali mission at the United Nations, said the court’s decision "probably will jam the courts" and was the result of "baseless lawsuits".
Mr Samantar was Somalia’s defence minister in the 1980s and prime minister from 1987 to 1990.
Source: BBC