Terrance "Terry" Williams now says he was sexually abused for years by the middle-aged man he beat to death in 1984 at the age of 18.
A unanimous vote was needed to recommend that Gov. Tom Corbett commute Williams' sentence to life imprisonment, but two of the five board members voted no.
None of the board members, who include state Attorney General Linda Kelly and Lt. Gov. Jim Cawley, commented following the vote. Kelly favored clemency and Cawley opposed it.
During two hours of often-emotional arguments and testimony in the state Supreme Court chamber at the Capitol, witnesses drew comparisons to Jerry Sandusky's victims in the Penn State child sex scandal to explain Williams' reluctance to publicly disclose the abuse.
"Going forward with this execution would be morally wrong," defense attorney Shawn Nolan told the pardons board.
Philadelphia prosecutors described Williams as a violent, calculating criminal who committed two robberies and another murder in a short period before he killed 56-year-old Amos Norwood with a tire iron, the crime for which he received the death penalty.
Tom Dolgenos, chief of federal litigation for the Philadelphia district attorney's office, said Williams initially sought to pin the murder on others and did not raise the issue of sexual abuse until 1998.
"The seriousness of the situation runs both ways," Dolgenos said.
Williams' co-defendant, Marc Draper, came forward with more information about the sexual abuse in January, Nolan said. Draper, who cooperated with authorities and received a life sentence, alleged that police and prosecutors told him not to mention the sexual abuse when he testified against Williams and to focus instead on the alleged robbery motive.
Although Williams has exhausted his appeals, he could win a reprieve if his lawyers can prove that prosecutors at his 1986 trial withheld evidence or interfered with his defense. A Philadelphia judge has scheduled a Thursday hearing to hear testimony from Draper and the prosecutor at Williams' trial.
Williams is scheduled to be executed Oct. 3.
Pennsylvania has executed only three men since the death penalty was reinstated in 1976, and all of them chose to end their appeals. There are 200 people on death row in the state.