In a unanimous decision, the court ruled in favor of Clarence Hill, who argued that the chemicals in lethal injection are too painful and would violate the Constitution's Eighth Amendment.
Lawyers for Hill cited a 2005 study in the Lancet medical journal that found that pancuronium bromide can cause suffocation and potassium chloride can cause burning in the veins and muscle cramping before death.
The court intervened in Hill's execution Jan. 24, staying his execution for the murder of a police officer as he was strapped to a gurney waiting for the lethal injection to be delivered into his arms.
The court's narrow ruling allows Hill to bring the challenge to a lower court, but did not address the merits of lethal injection.
Justice Anthony Kennedy, who wrote the court's opinion, also noted that while the case allows inmates to file similar special appeals, they will not always be entitled to delays in their executions.
"Both the state and the victims of crime have an important interest in the timely enforcement of a sentence," Kennedy wrote.
Many of the 37 states that use lethal injection in capital punishment had filed briefs with the court in favor of lethal injection, arguing that it would jeopardize justice for victims' families.
In Florida, Gov. Jeb Bush postponed all executions until the Supreme Court ruled on the issue.
"Hill's challenge appears to leave the state free to use an alternative lethal injection procedure," wrote Kennedy.
In another case involving a death-row inmate, the Supreme Court ruled 5-3 to allow Tennessee inmate Paul Gregory House to use new DNA evidence in a new hearing.
House was convicted and sentenced to death in 1985 for the murder of a female neighbor. DNA testing revealed that semen found on the victim's clothing belonged to her husband.
Kennedy, who also wrote the majority opinion, agreed with House's claim that new DNA and forensic proof, "has put forward substantial evidence pointing to a different suspect."
Justice Samuel Alito did not participate in the case since he was not yet on the bench when the case was argued in January.