The Supreme Court yesterday made it harder for minorities and women to challenge discriminatory job promotion and seniority systems.

In a 5-to-4 ruling, the court said those suing under federal civil rights law must meet the difficult burden of proving that a promotion and seniority system was intentionally discriminatory.

The justices struck down a lower court ruling exempting many seniority systems from this stiff requirement and allowing court-ordered remedies against systems just because they had a discriminatory effect, whether or not the bias was purposeful.

Yesterday's decision took on special importance because of the flood of layoffs now confronting the country in its economic crisis. Because of seniority systems, blacks and women, often the last hired, have been the first fired.

Had the court ruled the other way, labor lawyers said it would have produced a new onslaught of legal challenges to the systems which produced this disproportionate impact.

The ruling, written by Justice Byron R. White, can be altered by Congress, though that is considered unlikely.

Black employes of the American Tobacco Co.'s Richmond plants represented by the Legal Defense Fund of the NAACP brought yesterday's suit against a job progression plan implemented in 1968 as part of a collective bargaining agreement with the Bakery, Confectionery and Tobacco Workers International Union.

The effect of the plan was to create four job categories in which advancement was virtually sealed off to blacks because whites had always occupied the lower rungs. The blacks did not say the new plan was intentionally designed to exclude them from advancement: only that it extended the effect of past discrimination into the new job progression plan.

The court has ruled repeatedly that most job discrimination challenges under the Civil Rights Act of 1964 do not require a showing of discriminatory intent. Under such rulings, a hiring policy, for example, that is neutral toward minorities on its face can be found illegal because it excludes them in practice.

But in 1977, in a case involving the Teamsters Union, it ruled that Congress made a special exception for collectively bargained seniority systems. For them, intent must be proven.

The 4th U.S. Circuit Court of Appeals, however, ruled in yesterday's case, American Tobacco Co. et al v. Patterson et al, that the special exception applied only to seniority plans created before the effective date of the Civil Rights Act. The lower court cited legislative history to bolster its ruling.

White held yesterday that the lower court had misread the history. All seniority systems, whether created before or after the act, enjoy the special protection, he said.

The decision was an important victory for organized labor and the business community's Equal Employment Advisory Council, which had filed a "friend of the court" brief in support of what the court did yesterday. Labor and business lawyers said the 4th Circuit ruling, had it been applied nationwide, would have unleashed a whole new round of suits against seniority and promotion arrangements between labor and management.

The "effects" versus "intent" controversy goes beyond job discrimination law. The court has required the stiffer "intent" showing in voting rights, school desegregation and other cases.

The Reagan administration is urging Congress to ratify the court's requirement when it votes to extend the Voting Rights Act. Yesterday's decision, however, does not directly affect those controversies.

Justices William J. Brennan Jr., Thurgood Marshall, Harry A. Blackmun and John Paul Stevens dissented.

Brennan, Marshall and Blackmun said they favored a middle ground proposed in this case by the Equal Employment Opportunities Commission which allowed the stiffer standard for some systems but not for others.

Stevens said the job progression plan at issue was not a bona fide seniority system entitled to the special exception.

White, for the majority, said Congress wanted to "balance" the need for enforcement of discrimination laws with the need for "minimal supervision by courts and other governmental agencies over the substantive terms of collective bargaining agreements."

"It is not this court's function to upset that balance," he wrote. A contrary decision would conflict with the "plain language" of the Civil Rights Act's section on seniority plans, would be "inconsistent with our prior cases and would run counter to the national labor policy."

The complaint of the black workers in Richmond does not end with yesterday's decision. They now have a chance to argue that the American Tobacco job-progression plan is not, in fact, a seniority system and therefore can be challenged under the easier "effects" standard of the act.