The Supreme Court yesterday reaffirmed its ban on state-sponsored prayer in the public schools, striking down an Alabama law that required a moment of silence each day for meditation or prayer.

But the court, in a 6-to-3 ruling, indicated that most of the "moment of silence" laws enacted in 24 other states likely would pass constitutional muster. The Alabama law fell because it unconstitutionally endorsed religion as a "favored practice," the court said.

"The legislative intent of Alabama lawmakers to return prayer to the public schools is, of course, quite different from merely protecting every student's right to engage in voluntary prayer during an appropriate moment of silence," Justice John Paul Stevens wrote for the majority.

The decision, which represents a setback for President Reagan and various religious groups urging a return to organized school prayer, is likely to be more symbolically than legally important.

Civil liberties' lawyers say they receive complaints that many school districts nationwide violate the court's ban on official prayer, and yesterday's decision is unlikely to change that. The decision also breaks no legal ground, involving, as Stevens noted, a "narrow question" on the peculiarities of Alabama's law. The ruling in Wallace v. Jaffree shows, however, that a clear majority is not prepared to reverse Warren court rulings involving the separation of church and state.

A 1962 decision banned officially sponsored vocal prayer and Bible-reading in schools, partly because such activities implied state sponsorship of religion or of one religion over others.

The court, Stevens said yesterday, "has unambiguously concluded that the individual freedom of conscience protected by the First Amendment embraces the right to select any religious faith or none at all."

Reaction to the ruling was quick and emotional.

The Rev. Jerry Falwell, founder of the Moral Majority, said the six justices in the court majority "don't understand what freedom's all about."

Tim LaHaye, of the conservative American Coalition for Traditional Values, called it a "tragic day in American history," adding that the decision represents a "breakdown in values when we need recognition of God most." Alabama Gov. George C. Wallace said he was "disturbed and disappointed" by the ruling.

Former solicitor general Rex E. Lee, who on behalf of the Reagan administration urged the court to uphold the Alabama law, said he saw a "victory in that moment-of-silence statutes in general will survive."

Burt Neuborne, spokesman for the American Civil Liberties Union, said he was "delighted" by what he called a "very traditional ruling and a very conservative opinion. What is courageous is that the court did not back away" from its previous rulings on the separation of church and state, he said.

Various religious organizations praised the decision. James M. Dunn of the Baptist Joint Committee called the decision "proper" and well-founded.

National Council of Churches President Dean Kelly said the decision was "what the court should have decided . . . . The court has held that it is not the business of the government to sponsor prayer . . . in public schools. That's not to say children can't pray in the way Jesus said in the Sermon on the Mount -- which is in their hearts." Jewish leaders also praised the ruling, calling it an important reaffirmation of past decisions.

Four justices, William J. Brennan Jr., Thurgood Marshall, Harry A. Blackmun and Lewis F. Powell Jr., joined Stevens' opinion in full. Justice Sandra Day O'Connor concurred, agreeing that the Alabama statute was a constitutionally "impermissible endorsement of prayer in public schools."

O'Connor, a Reagan appointee, said Alabama had "intentionally crossed the line between creating a quiet moment during which those so inclined may pray and affirmatively endorsing the particular religious practice of prayer.

"This line may be a fine one, but our precedents and the principles of religious liberty require that we draw it," O'Connor said.

Chief Justice Warren E. Burger, in dissent, said the emotional debate sparked by the case could be viewed as " 'much ado about nothing,' since no power on earth -- including this Court and Congress -- can stop any teacher from opening the school day with a moment of silence for pupils to meditate, to plan their day -- or to pray if they voluntarily elect to do so."

"The notion that the Alabama statute," because it specifically mentions "prayer" is "a step toward creating a state church borders on, if it does not trespass into, the ridiculous."

Justice Byron R. White, in a separate dissent, said he agreed for the most part with Burger.

"A majority of the court would approve statutes that provided for a moment of silence that did not mention prayer," White said. "But if a student asked whether he could pray during that moment, it is difficult to believe that the teacher could not answer in the affirmative."

Justice William H. Rehnquist, also in dissent, argued that the Alabama law should be upheld because no part of the Constitution "prohibits any such generalized 'endorsement' of prayer" although it prohibits endorsing one religion over another.

Maryland and Virginia have laws permitting a moment of silence. The District of Columbia has no school prayer statute.