In a break with more than half a century of history, El Salvador's new government will have a provisional president, vice president and Cabinet ministers in the American pattern rather than a civilian-military junta, politicians negotiating the arrangement said today.

The five parties that won legislative seats in last Sunday's elections have agreed on little else in three days of private talks, during which they have been wrangling over the structure of the government that will draw up a new constitution and move the country toward presidential elections within the next few years. Who will hold the new posts is still being debated.

The decision to exclude the armed forces from a formal role is a major one, reflecting both the civilians' determination to move toward a fully democratic system and a military decision to let them do it. Although U.S. officials are known to have favored this course, the sources agreed that military willingness and not U.S. pressure on the civilians was the main reason for the agreement.

"This is what we all wanted and one way we can all work together," said Francisco Jose Guerrero, head of the National Reconciliation Party and among those likely to be named to a high post. Talks just after the election had considered setting up a junta with one military member, similar to the four-member council that now runs El Salvador.

The armed forces, who installed the current government in a 1979 coup, have had a hand in every government since 1931. They will still retain control through the Department of Defense over internal security matters and the continuing warfare against leftist rebels, and they will probably be allowed to choose the defense minister, according to sources involved in the talks.

At the moment, Defense Minister Gen. Jose Guillermo Garcia is considered the most powerful individual in the country and it is likely he will remain in that post. Military officials refused to speculate.

But the Army will not be sharing formal executive power with the president, even though no one believes it will break its interventionist tradition and stand idle if the politicians prove unable to govern effectively. In every public appearance, politicians on all sides have warned that the elections were only the first step toward a civilian government.

While the politicians were working to form a new government, leftist guerrillas fought government troops for six hours last night in the provincial capital of San Vicente, military sources said. The rebels also raided the provincial capital of San Francisco Gotera, blew up a bridge, overran an Army outpost and cut two key highways and phone lines to nine towns. The Army outpost was later retaken, military sources said.

At least one official close to the negotiations said retired major Roberto D'Aubuisson, head of the rightist Nationalist Republican Alliance, known as ARENA, its Spanish abbreviation, had been chosen to become minister of the interior, although other sources said that this was only tentative.

The Interior Ministry, one of the most powerful, is responsible for dispensing funds and project permits to local officials.

Guerrero said in an interview that the talks now concern which parties will control which ministries, and who will name the assistant ministers.

"We're trying to build a system of balances that will still be able to function," he said.

U.S. Ambassador Deane Hinton had warned the politicians that putting D'Aubuisson in a highly visible post would jeopardize the continued flow of U.S. aid because of his history as a plotter of coups and his reported ties to death squads. But recently Hinton's tone has softened as D'Aubuisson's fortunes have risen, and the State Department lifted its previous objections to allowing him to visit the United States. In clear deference to U.S. objections, ARENA has not even suggested that D'Aubuisson be president, officials here said.

An official close to the talks said Fidel Chavez Mena, foreign minister under the current government headed by the Christian Democratic Party, would remain in that post, but the report could not be confirmed. He is widely regarded as a peacemaker acceptable to all sides, but it is known that the Christian Democrats would like to see him as vice president.

Negotiations are not even addressing the question of a job for President Jose Napoleon Duarte, the sources said, because his ouster remains one of the few things uniting the four rightist parties who together won a 60 percent majority of the election's 1.3 million votes. Duarte has indicated he will step down if his party asks him to do so.

The role of the Christian Democrats in the new government is the most controversial issue, since the rightists' coalition is very loose at best, and the Christian Democrats have said they must have power in proportion to their 40 percent of the vote to keep their backers from becoming rebellious. Key actors on all sides of the political drama are foregoing the Holy Week vacations that are traditional in this largely Roman Catholic country to keep the talks going.