He is accused of commanding his troops to detain, torture, and kill members of Somalia's Isaaq clan.
The court ruling means that the Somalis who have brought the case will for the first time be able to question him.
A lawyer for Mr Samantar argued on Friday that the case against him should be thrown out.
But US District Judge Leonie Brinkema denied the request to dismiss it.
The original lawsuit was filed in 2004 by Somalis living in the US under 1991's Torture Victim Protection Act.
A federal judge later ruled that Mr Samantar was entitled to diplomatic immunity, but last year the US Supreme Court reinstated the case.
Earlier this year, the US Department of State recommended that Mr Samantar should not receive diplomatic immunity, largely because there was no effective central government in Somalia to request it.
Somalia has not had a functioning national government since warlords overthrew President Siad Barre, under whom Mr Samantar served, in 1991