The stay, which was issued about 4 hours before Manning's scheduled execution, will remain in effect until the high court issues a further order, WDAM-TV, Hattiesburg, reported.
The TV station said Justice Michael Randolph disagreed with the decision, citing various legal and factual reasons in his dissent.
The stay came after the U.S. Justice Department sent three letters calling into question certain aspects of trial testimony by two FBI experts.
Mississippi Attorney General Jim Hood said in a statement the Supreme Court acted to allow more time to review a "flurry of last-minute filings." He said the Justice Department letters did not mean the FBI agents' testimony was inaccurate.
"I am sorry that the victims' families will have to continue to live this 20-plus-year nightmare," Hood said.
Manning was convicted of killing Mississippi State University students Tiffany Miller of Madison County and Jon Steckler of Natchez in 1992. Both were found shot in the head.