The Senate yesterday joined the House in approving legislation to prohibit most polygraph tests by private employers as the Democratic-controlled Congress stepped up election-year action on labor-related bills.

The Senate approved the polygraph measure, 69 to 27, after a coalition led by Sens. Edward M. Kennedy (D-Mass.) and Orrin Hatch (R-Utah), normally foes on labor issues, easily overcame filibuster threats and opposition from conservatives usually allied with Hatch.

The bill, which would ban employers from using polygraph tests to screen job applications and to make random checks of workers' honesty, now goes to conference committee to resolve differences with the stronger House version, which would impose an even wider prohibition on use of the devices.

Sen. Dan Quayle (R-Ind.), who led the fight against the Senate measure, predicted that President Reagan will sign the legislation despite administration objections to some provisions in both the House and Senate versions. "They {the administration} have folded like a house of cards and will not veto this bill," Quayle said.

Kennedy predicted the measure will be enacted with or without Reagan's signature, even though the 254 to 158 vote in November by the House on its version of the bill fell short of the two-thirds majority that would be needed to override a veto.

"We applaud the Senate in recognizing that lie detectors can be used in blatant assaults on a worker's right of privacy," AFL-CIO President Lane Kirkland said in a statement.

The House bill would ban all use of polygraph tests in private employment except for security personnel and employees of pharmaceutical companies.

While the Senate bill would ban indiscriminate testing of employees and job applicants in most kinds of work, it would permit such testing at nuclear power plants, security firms and armored car companies under an amendment sponsored by Sen. Don Nickles (R-Okla.) and accepted by Kennedy.

The Senate measure also would allow use of polygraphs as part of an investigation of specific incidents, such as theft, embezzlement or sabotage, so long as the testing conformed with procedural safeguards set by the Labor Department.

But employers would be barred from disciplining workers solely for refusing to take a polygraph test and from asking questions related to religion, sex, political beliefs or attitudes toward labor unions. Questions would have to be supplied in advance. And a worker could terminate the test at any time. Employers would be required to post notices about the bill's provisions or be fined $100 a day for failure to do so. Fines of up to $10,000 would also be imposed for violating the legislation itself.

Charging that polygraph tests have become the "witchcraft" of the 20th century, Kennedy contended that tests are proliferating even though studies have shown them to be unreliable. He called them "inaccurate instruments of intimidation."

In the 2 million tests administered every year, 320,000 "honest Americans are branded as liars," said Hatch, contending that failure to pass a polygraph test, however unfair, gives workers a "stigma they'll wear for life like a scarlet letter."

Opponents charged that federal constraints would be an unwarranted intrusion on state powers and, while conceding there are problems, defended the tests as a deterrent to theft and other wrongdoing in the workplace. "Once again, we're saying Washington knows best," Quayle said.

While Hatch joined Kennedy on the polygraph measure, he warned that his support will not extend to many of the other labor-related measures that Kennedy and other liberal Democrats are hoping to pass this year despite filibuster threats in the Senate and veto threats from the White House.

Several job-protection measures have been included in the omnibus trade bill now in House-Senate conference. And others have been passed by the House, including a bill to require notification of workers who are exposed to health hazards.

Legislation to raise the minimum wage for the first time in nearly a decade is pending in both houses. And the Senate is expected soon to consider that measure along with Kennedy-sponsored legislation to require all employers to provide a minimum level of health insurance.

Legislation is also pending in the House to require employers to provide leave, with job protection, for new parents and disabled workers.