President Alberto Natusch Busch, the Army colonel who seized power two weeks ago from Bolivia's first democratically elected president in a decade, agreed early today to step down immediately.

Defense Minister Gen. Oscar Larrain emerged from a meeting with congressional leaders to announce that a new president will be selected, apparently by the Congress, later today.

Natusch's troops had multiplied popular opposition to his rule by their bloody repression of civilians who took to the streets in protest against the Nov. 1 coup. It also drew sharp denunciation from the Carter administration, which earlier had cited Bolivia's return to civil rule as a model for other military governments in Latin America.

The Bolivian Human Rights Commission declared yesterday that 207 civilians were killed, 201 wounded and 211 missing after detention by security forces in the week following the coup.

The announcement early today indicated that both Natusch and civilian lawyer Walter Guevara Arze, the constitutional president he displaced, will resign their claims and allow the Congress to choose a third man.

A close aide to Natusch said the colonel submitted his resignation to his general staff in order to achieve peace in Bolivia.

Natusch has encountered widespread opposition from the Congress, unions, the Catholic church, human rights groups and students.

Representatives of the armed forces who had been negotiating with Congress for several days had said the military would agree to "any solution" that did not include Natusch or Guevara.

It was not known immediately what kind of government would emerge. Both a military-civilian triumvirate and the turning over of power to the Congress have been suggested.

The solution will be announced formally this afternoon, said the president of the Congress, Lidia Gueiler, after four hours of talks with the armed forces emissaries.

"The National Congress has the last word. All obstacles have been overcome, and congress will define today the constitutional way out of the crisis," Gen. Larrain said.

The Bolivian Workers' Confederation last night rejected a proposal to enter into a tripartite administration with the military and parliament. It held that parliament alone should appoint a government.

There was no immediate reaction from Natusch, who was holed up in the Quemado presidential palace across where the congressional leaders met and agreed to remove him.

Larrain's statement, made just after midnight, came after a day in which rumors swirled that Natusch would be overthrown in a coup. There were unconfirmed reports an air force unit had rebelled and troops and tanks surrounded an air force base at El Alto airport. The government immediately denied the reports.

At the same time, two military officers read a manifesto they said was signed by 250 officers that called on Natusch to resign and return power to a civilian government.

They said, "We are not alone because 90 percent of our comrades in the armed forces will follow our steps until we return to the people that which is rightfully theirs."

About 3,000 students marched from the National University to a La Paz cemetery yesterday in a rally honoring the persons slain by soldiers in the coup that ousted Guevara.

Many shook their fists and shouted "Murderer! Murderer!" as they passed government buildings. Police watched but did not intervene.

Bolivia's 22 Roman Catholic bishops issued a statement saying they Condemn the violent repression that resulted in a great number of deaths, wounded and disappearances in our country."

Only Egypt and Malaysia had recognized the Natusch government. The United States and Venezuela cut economic assistance to Bolivia, and the pressure was being felt.

The central bank ordered all banks closed yesterday and today, and private banking sources said a devaluation of the Bolivian peso -- now pegged at 20 to the dollar -- would be forthcoming. The sources said the central bank is broke and Bolivia must pay $300 million in capital and interest on loans by Jan. 1.