Just hours after a federal appeals court halted the preparations, the high court agreed, preventing Hubert Lester Michael Jr. from becoming the first person put to death in the state since 1999.
Michael, 56, who pleaded guilty to fatally shooting Trista Elizabeth Eng in 1993, had been taken earlier in the day to Rockview State Prison in Bellefonte, home of the execution chamber.
Pennsylvania has put to death only three inmates in the past 50 years, and all of them - unlike Michael - had given up on their appeals.
Prison officials described Michael as "very quiet, polite and composed" during what were to have been his final hours. He arrived there shortly after 6 a.m., after being transported from Greene State Prison in the state's southwestern corner.
After the Supreme Court decision, one of Michael's lawyers, Helen Marino, said he remained "incredibly remorseful" that he had killed Eng.
Marino said the courts saw there were "compelling claims relating to Mr. Michael's debilitating mental conditions that have never been reviewed by any court."
Sue McNaughton, a spokeswoman for the Corrections Department said, "If and when the stay is lifted by the court, the execution will be scheduled directly."
Earlier Thursday, the 3rd U.S. Circuit Court of Appeals sent the case back to a district court judge to address, among other things, whether Michael's appeal should be considered a successive petition that is subject to stricter rules, whether "extraordinary circumstances" existed and whether a district court proceeding is needed to consider the merits of Michael's claims.
Prosecutors argued in vain to the Supreme Court that that decision was in error.
"An examination of this case leads to the inexorable conclusion that Michael simply is not entitled to relief," wrote Chief Deputy Attorney General James P. Barker.
But Michael's lawyers argued that his claims that his federal rights have been denied deserved more attention in the lower courts.
Since he was sentenced to death, Michael had abandoned his appeals but later resumed a legal fight, saying he had been confined under circumstances at Graterford State Prison that worsened his mental health problems. Those problems got better after he was transferred to Greene, his lawyers have argued.
In a filing Thursday, the attorney general's office said Michael is pursuing a "successive" federal appeal that is subject to more strict court rules.
"Michael's entire argument was that, since the time of his voluntary waiver, the circumstances of his confinement have improved and effected some concomitant amelioration of his spirit. He has developed relationships ... and he has changed his mind," prosecutors wrote. "Even if true, this argument is in no way similar to a complaint of error at the district court proceeding based on failure to exhaust, procedural default, or the relevant statute of limitations."
Pennsylvania has just over 200 people on death row, the fourth most of any state after California, Texas and Florida.
The lack of executions has been attributed to a number of factors and debated for years in the state's legal circles. Prosecutors claim an anti-death penalty bias on the part of appeals judges, while defense attorneys note many of the sentences have been proved to be flawed and overturned on legitimate legal grounds.
While the courts were deciding Michael's fate Thursday night, about a dozen protesters gathered along the highway in front of the sprawling prison complex.
"It's definitely a relief," said Patrick Klinger, a member of the group called Pennsylvanians Against the Death Penalty. "Relief, but with a heavy heart because we might be back up here in two weeks."
At a 1997 hearing in Michael's case, his former public defender testified that Michael told him how he picked up the girl hitchhiking, bound her with electrical cord stolen from her home, raped her and killed her on state game land.
He was not charged with rape because of a lack of physical evidence, though prosecutors suspected it. Michael confessed to his brother, who located her remains about a month after she disappeared and called police. She had been shot in the head and chest.
At Wednesday's pardons board hearing, the victim's mother, Suzanne Eng, set the tone for relatives and friends who made emotional pleas to keep the execution on track.
"He kidnapped her, he raped her and then he executed her," the mother said. "As she begged him not to kill her, he shot her three times."
Associated Press writer Genaro C. Armas contributed to this report.