But confusion still reigns over just what the Constitution allows, and school officials nationwide remain caught in the middle of what the National School Boards Association calls "religious warfare."
The justices, acting without comment, let stand rulings that declared the 1994 Mississippi law a violation of the constitutionally required separation of church and state.
Yesterday's action was not a ruling on the merits of the Mississippi law and set no national precedent. But it was a defeat for Mississippi officials who had hoped to revive the state law.
The action also could be a setback for those outside Mississippi who argue that student-initiated prayers are constitutional in various public school settings.
"I hope lower courts won't read into the court's action any disapproval of legitimate student-initiated prayer and worship, such as prayer clubs," said Jay Sekulow of the American Center for Law and Justice.
"The way the (Mississippi) statute was worded was problematic at the outset," Sekulow said. "Official sanction was all over it."
The invalidated Mississippi law would have allowed "invocations, benedictions or nonsectarian, non-proselytizing student-initiated voluntary prayer" at "school-related student events."
T. Hunt Cole Jr., the special assistant attorney general who had filed the state's spurned high court appeal, said, "Our arguments on constitutional issues are over. There's nothing more we can do."
Republican leaders in Congress have proposed amending the Constitution to allow more opportunities for prayer in public schools. President Clinton says such an amendment is unnecessary, but Republican nominee Bob Dole supports it.
Since a 1962 Supreme Court ruling, organized school prayers have been barred from public schools. But that landmark case involved prayer sessions sponsored and led by public school officials, not students.
The court, of course, never has banned individual prayer from public schools. Students remain free to pray before lunch, before tests or even during class if they do so in an unobtrusive way.
The justices in 1992 strengthened the ban on officially sponsored worship in public schools by prohibiting clergy-led prayers at public school graduation ceremonies.
But the 5th U.S. Circuit Court of Appeals - in a decision that still is binding law in Mississippi, Louisiana and Texas - subsequently ruled that the 1992 decision did not apply to graduation prayers planned and led by graduating seniors.
The Supreme Court silently left that ruling intact in 1993. But another federal appeals court has declared such student-led graduation prayers unlawful.
The National School Boards Association last year told the justices in another dispute that the nation's public schools "are currently the site of religious warfare" and that "school boards are caught in the middle and do not know which way to turn."
Contacted yesterday, NASB Executive Director Anne Bryant said "a lack of clarity from the courts" was "forcing school boards to be judges and juries - not a good place for them to be."
"What school boards across the nation would love is to have the Supreme Court give us some guidance," she said. "The murky area still haunts us, especially at graduation time."
The Mississippi law, designed to go beyond graduation ceremonies, was enacted shortly after a widely publicized incident in which a Jackson high school principal was disciplined for allowing students to recite prayers over the school public address system while students were required to be in their classrooms.
David Ingebretsen, executive director of the state American Civil Liberties Union, and his daughter were among 14 individuals who sued to block the law from taking effect.
U.S. District Judge Henry Wingate ruled that the law was unconstitutional, except when applied to graduation ceremonies.
A three-judge panel of the 5th Circuit court upheld his ruling, and the entire appeals court voted 9-6 not to reconsider that ruling.
Leading the dissenters, Judge Edith Jones said the trial judge went too far in "striking down Mississippi's attempt to accommodate students' desire - and constitutional right - voluntarily to pray aloud at school" before it ever had been invoked by any student.
In the appeal acted on yesterday, Mississippi Attorney General Mike Moore argued that the law "does not mandate than any religious speech or prayer occur at all at any time." Instead, he said, "this is left to private choice."
Opponents of the law urged the justices to reject the state's appeal, saying that the lower court rulings did nothing "to deprive any students of any independently existing constitutional right to pray in public schools."