Robin Lovitt, 41, had been scheduled for execution at 9 p.m. Monday.
The stay will remain in place until the court returns in October from a three-month break. Justices will announce then whether they will hear Lovitt's appeal or allow Virginia to execute him.
Attorneys for Lovitt had sought a last-minute appeal from the high court and requested clemency from Gov. Mark R. Warner. Among those fighting the execution are former independent counsel Kenneth Starr, who argued the case before the 4th U.S. Circuit Court of Appeals in February.
Lovitt's case attracted national attention because the murder weapon and DNA evidence were destroyed after the trial.
"We're just glad that reason has come to light," said Jack Payden-Travers, executive director of Virginians for Alternatives to the Death Penalty. "Had the execution gone ahead it (would have been) a miscarriage of justice."
Lovitt was convicted in 1999 in the slaying of Clayton Dicks, 44, during a pool hall robbery in Arlington.
Lovitt's lawyers and opponents of capital punishment have argued that the conviction should be reviewed because of the questions surrounding the evidence.
Initial DNA tests of the bloody scissors could not conclusively link Lovitt to the 1998 slaying. A court clerk later destroyed most of the evidence, including the scissors, making additional DNA testing impossible.
The Virginia attorney general's office has maintained that DNA evidence was not critical to the conviction because of "very compelling, strong evidence," including eyewitness testimony.