The Supreme Court, over the vigorous protests of the Reagan administration and private industry, yesterday opened up important new opportunities for minorities to challenge hiring and promotion procedures under federal job discrimination laws.

In a 5-to-4 ruling, the court said that even an employer with an excellent overall minority employment record can be found guilty of discrimination if just one part of his personnel system, such as testing, is unfair to blacks.

The decision, which originated with a complaint against a written examination given by an agency of the state of Connecticut, rejected the contention that employers should be judged exclusively by the "bottom line" in employment cases.

For employers, the decision eliminates an important defense not only against complaints about tests, but also against complaints about job application procedures, performance appraisals, educational requirements and any other step along the way to the final decision on whom to hire, transfer or promote.

In another significant ruling yesterday, the court said that virtually all of its decisions on what constitutes illegal search and seizure will apply retroactively. Under the court's ruling, any new interpretation by the justices could result in numerous criminal convictions' being thrown out across the country even though they were based on evidence properly adjudged admissible at the time of trial. However, the retroactivity only applies to those defendants still in the process of appealing their convictions.

The decision involves the controversial "exclusionary rule," under which illegally seized evidence may be excluded from a criminal trial. The 5-to-4 judgment appeared to be a defeat for advocates of a "good faith" exception to that rule.

The employment discrimination case began with a complaint brought by four black employes of the Connecticut Department of Income Maintenance under Title VII of the Civil Rights Act of 1964. The employes said a promotion examination used in that department was biased against blacks because they passed it at only 68 percent of the rate for white candidates. Specifically, 26 of the 48 blacks who took the test passed while 206 of the 259 whites passed.

State officials, however, said they had promoted blacks who passed the test at a much greater rate than the whites: about 23 percent of the blacks who passed but only 13 percent of the whites ultimately got promotions. This, the state said, was the "bottom line," and it was the bottom line that really mattered.

But in yesterday's decision affirming the 2nd U.S. Circuit Court of Appeals, Justice William J. Brennan said the individual blacks who failed the test and brought the complaint did not get promotions, so although other blacks did, that does the four no good.

The anti-discrimination law is designed to protect individuals, Brennan wrote in Connecticut et al. vs. Teal. "The principal focus of the statute is the protection of the individual employe, rather than the protection of the minority group as a whole," he said.

"It is clear that Congress never intended to give an employer license to discriminate against some employes on the basis of race or sex merely because he favorably treats other members of the employes' group," Brennan wrote.

Justice Lewis F. Powell Jr., joined by Chief Justice Warren E. Burger and Justices William H. Rehnquist and Sandra Day O'Connor dissented, saying the majority had misconstrued prior rulings of the court.

"By its holding today," Powell wrote, "the court may force employers either to eliminate tests or rely on expensive, job-related, testing procedures . . . . For state and local governmental employers with limited funds, the practical effect of today's decision may well be the adoption of simple quota hiring," he said.

The Justice Department, in a friend of the court brief, had sided with Connecticut in the dispute. Brennan noted that the Equal Employment Opportunity Commission had apparently been in disagreement with the department and had dissociated itself from the brief.

The ruling concerning retroactivity in search and seizure cases is an attempt to create a clear rule after years of confusion and case-by-case decisions on the subject. The appeal before the court grew out of a May, 1977, incident during which Secret Service agents made a warrantless search and arrest at the Los Angeles home of Raymond Eugene Johnson. Based on the evidence taken, Johnson was convicted of intercepting a government check. Appeals courts allowed use of the evidence.

In April, 1980, the Supreme Court ruled in an unrelated case--Payton vs. New York--that such warrantless entries violated Fourth Amendment prohibitions on unreasonable search and seizure.

Yesterday, Justice Harry A. Blackmun, writing for the 5-to-4 court in U.S. vs. Johnson, said the Payton ruling applied to Johnson's case. Retroactivity, he said, applies from now on to most Fourth Amendment search and seizure cases so long as the defendant has not exhausted his final appeal.

In a third case, Patsy vs. Board of Regents of the State of Florida, the court ruled 7 to 2 that federal judges may rule on civil rights damage suits against state officials without waiting for state administrative agencies to consider the complaints.

Civil liberties lawyers had feared that an opposite ruling could have had a severe delaying effect on the ability of victims to remedy violations of individual rights. Justice Thurgood Marshall, writing for the court, said the law in question--Section 1983 of the Civil Rights Act of 1871--was created to provide swift redress for constitutional violations.

He based his decision on a law Congress passed in 1979 requiring prison inmates to exhaust most administrative remedies before complaining about prison conditions under the same civil rights law in federal court.

By excepting this one group, Marshall said, Congress signaled its view that exhaustion of state administrative remedies is not required for others.

Powell dissented, saying the Florida suit was prohibited by the Eleventh Amendment to the Constitution, which bars federal damage suits against state governments. O'Connor, joined in a separate concurrence by Rehnquist, took the opportunity to repeat previous off-the-bench comments recommending that Congress change the law to require the use of state administrative channels before allowing federal intervention.