In a brief statement, Justice Anthony Kennedy said on Wednesday he had responded to a request by Idaho's Republican governor, Butch Otter.
Kennedy issued his ruling just 90 minutes before Idaho would have been able to begin allowing gay marriages.
The order is an administrative one and will apply only until the high court takes further action on the matter.
Otter requested the suspension due to the potential risks of "chaos, confusion, conflicts and uncertainty" that, in his judgment, could have beset local administrations if same-sex marriages had been allowed.
Kennedy's suspension initially applied to Nevada as well, but at mid-afternoon on Wednesday, he clarified that his earlier order to block gay marriages applied only to Idaho, according to the governor's request.
On Tuesday, the 9th Circuit Court of Appeals in San Francisco, which has jurisdiction over Idaho and Nevada, overturned the prohibitions on gay unions in those states.
Kennedy, the justice designated to respond to emergency requests presented by the states covered by the 9th Circuit, said that now the plaintiffs involved in Idaho's gay marriage lawsuit must present a response by the end of the day on Thursday.
The overturning of the gay marriage laws in the two states would mean the de facto recognition of same-sex marriage there.
The gay marriage issue has had a significant impact on the US justice system this week after the Supreme Court Monday refused to rule on legalisation of such unions nationwide.
The high court also rejected the appeals of five states - Virginia, Oklahoma, Utah, Wisconsin and Indiana - who were seeking to prohibit same-sex marriages.