A congressman from Chicago and a prominent civil rights leader were arrested yesterday at the embassy of South Africa in the second of what sponsors said will be a continuing series of demonstrations aimed at changing policies of the white-minority-controlled country.

While about 150 chanting demonstrators marched nearby, Rep. Charles Hayes (D-Ill.) and the Rev. Joseph Lowery, head of the Southern Christian Leadership Conference, were taken into custody by uniformed Secret Service officers. The Secret Service said the officers were called by the embassy.

A spokesman for the two demonstrators said they were arrested "after it was apparent that they wouldn't leave" until they saw Ambassador Bernardus G. Fourie.

Hayes, 66, and Lowery, 59, were led from the building in handcuffs and taken to the 2nd police district station where they were charged with unlawful entry, a misdemeanor. After declining release pending a court appearance, they were taken to the cellblock at police headquarters to await arraignment.

"I just couldn't sit idly by and not offer my support . . . to try to end the . . . atrocious situation in South Africa," Hayes said before he and Lowery entered the embassy at 3051 Massachusetts Ave. NW.

Lowery said protesters "are prepared to have people arrested every day to raise national consciousness about this problem."

Last Wednesday, D.C. Del. Walter Fauntroy and two other black leaders were arrested at the embassy in a sit-in there. After spending the night in custody, they pleaded innocent to charges of unlawful entry and were released pending a hearing.

On Friday, Fauntroy, U.S. Civil Rights Commission member Mary Frances Berry and Randall Robinson, director of the lobbying group Trans-Africa, said they were forming a new "Free South Africa Movement."

They said it was aimed at pressuring the Reagan administration to alter its policy toward South Africa and said the group would sponsor or coordinate a program of "direct action" including sit-ins and demonstrations at the embassy and at South African consulates.

After participating for a time in the demonstration that was held about a block south of the embassy, Lowery and Hayes walked to the door of the building at about 4:20 p.m., appeared to ring a bell and were admitted to a vestibule.

Around 5:30 p.m., after a brief discussion with someone inside the embassy, the two men were led silently out.

Protesters said an immediate goal was winning the release of 13 South African labor union leaders who have not been heard from since their arrest during a two-day strike Nov. 5 and 6.

A White House spokesman defended the administration's policy toward South Africa, saying it was used throughout the president's first term, which he said saw "some notable achievements as far as improved relations between South Africa" and neighboring states.