Dominique Ray, 42, was pronounced dead at 10:12 p.m. of a lethal injection at the state prison in Atmore.
Ray had argued Alabama's execution procedure favors Christian inmates because a Christian chaplain employed by the prison typically remains in the execution chamber during a lethal injection, but the state would not let his imam be there in the room.
Attorneys for the state said only prison employees are allowed in the chamber for security reasons.
Ray's imam, Yusef Maisonet, watched the execution from an adjoining witness room, after visiting with Ray over the past two days. There was no Christian chaplain in the chamber, a concession the state agreed to make.
Strapped to a gurney in the death chamber, Ray was asked by the warden if he had any final words. The inmate said an Islamic statement of his faith in Arabic.
The 11th U.S. Circuit Court of Appeals on Wednesday had stayed the execution over the religious arguments, but the U.S. Supreme Court allowed it to proceed in a 5-4 decision Thursday evening. Justices cited the fact that Ray did not raise the challenge until Jan. 28 as a reason for the decision.
Justice Elena Kagan wrote in a dissent that she considered the decision to let the execution go forward "profoundly wrong."
Other states generally allow spiritual advisers to accompany condemned inmates up to the execution chamber but not into it, said Robert Dunham, executive director of the Death Penalty Information Center, which studies capital punishment in the United States.
Durham said did not know of any other state where the execution protocol calls for a Christian chaplain to be present in the execution chamber.
Alabama Corrections Commissioner Jeff Dunn said this is the first time the state has had an objection to the chaplain's presence. He said the state will review procedures to determine if something needs to be changed.
Ray was sentenced to death for the 1995 rape and murder of a 15-year-old girl. Tiffany Harville disappeared from her Selma home on July 15, 1995, and her decomposing body was found one month later in a cotton field.
It was Alabama's first execution of the year.
Ray was convicted in 1999 after another man, Marcus Owden, confessed to his role in the crime and implicated Ray. Owden told police that they had picked the girl up for a night out on the town and then raped her. Owden said that Ray cut the girl's throat. Owden pleaded guilty to murder, testified against Ray and is serving a life sentence without parole.
A jury recommended the death penalty for Ray by an 11-1 vote.
Ray's attorneys had also asked in legal filings to stay the execution on other grounds. Lawyers said it was not disclosed to the defense team that records from a state psychiatric facility suggested Owden suffered from schizophrenia and delusions. The Supreme Court also rejected the request.
Spencer Hahn, one of Ray's attorneys, said he was appalled that Ray received unequal treatment at his death because he was a member of a religious minority,
"Domineque was a devout Muslim and a human being. He was a son, a father, a brother. He wanted equal treatment in his last moments," Hahn wrote in a statement.
Ray's legal team said his first name was Domineque. The prison system used a different spelling, citing court records.
Alabama Attorney General Steve Marshall issued a statement saying he was pleased the court let the execution proceed.
"For 20 years, Domineque Ray has successfully eluded execution for the barbaric murder of a 15-year-old Selma girl. ...Tonight, Ray's long-delayed appointment with justice is finally met," Marshall said.
