Justice Alito joined five members of the court in blocking the execution of the inmate, Michael Taylor, who had argued that lethal injection is cruel and unusual punishment, a claim also used by two Florida death-row inmates that won stays from the Supreme Court over the past week.
Chief Justice John G. Roberts Jr. and Justices Antonin Scalia and Clarence Thomas voted to lift a stay that Mr. Taylor had won from an appeals court earlier in the evening.
The court has agreed to use one of the lethal-injection cases to clarify how inmates may bring last-minute challenges to the way they will be put to death.
Earlier in the day, Justice Alito was sworn in for a second time in a ceremony at the White House, where he was lauded by President Bush as a man of "steady demeanor, careful judgment and complete integrity."
He was also was given his assignment for handling emergency appeals: Arkansas, Iowa, Minnesota, Missouri, Nebraska, North Dakota and South Dakota. As a result, Missouri filed with Justice Alito its request for the court to void a stay and allow Mr. Taylor's execution.
The court's split vote Wednesday night ended a frenzied day of filings. Missouri twice asked the justices to intervene and permit the execution, while Mr. Taylor's lawyers filed two more appeals seeking delays.
Reporters and witnesses had gathered at the state prison awaiting word from the court on whether to go ahead with the execution.
Mr. Taylor was convicted of killing 15-year-old Ann Harrison, who was waiting for a school bus when he and an accomplice kidnapped her in 1989. He pleaded guilty and said he was high on crack cocaine at the time.