A split in the American Presbyterian church at the beginning of the Civil War was healed formally today when the northern and southern churches reunited to become the fourth largest Protestant denomination in the country.

Climaxing negotiations that go back nearly half a century, the commissioners, as delegates are called, voted out of existence the 823,143-member Presbyterian Church in the United States, the southern body, and the 2,351,119-member United Presbyterian Church in the U.S.A., the northern church.

Then they celebrated with a joyous mid-afternoon procession through the streets to Atlanta's City Hall, where they were hailed by Mayor Andrew Young.

In a setting of pageantry and worship tonight at Georgia's World Congress Center, the two moderators of the uniting churches read the declaration constituting the new Presbyterian Church (U.S.A.).

"By virtue of the authority vested in us, we declare . . . the Presbyterian Church (U.S.A.) is now constituted as part of the one holy, catholic and apostolic church of our Lord and savior, Jesus Christ," intoned the Revs. James H. Costen of the northern church and John Anderson of the southern church.

Even though it was the beginning of the communion service, the thousands of commissioners and observers gathered from all over the country stood, applauded and cheered.

Three long tables at the front of the center were piled with loaves of bread and chalices of every shape and description, which the commissioners had brought from their congregations.

The new church will hold its first business meeting Saturday and elect a moderator. That highest elective Presbyterian post is widely expected to go to the Rev. Dr. John Randolph Taylor of Charlotte, N.C., formerly a pastor at the Church of the Pilgrims in Washington.

The vote in the southern church to "formally approve full organic union" appeared to be unanimous. In the United Presbyterian assembly, there was at least one dissenter.

Deborah Kapp of Chicago said after the session that she had voted "no" because she was uneasy about provisions for affirmative action for women and for racial minorities. But she added that she would continue to "work effectively and faithfully" in the church.

In both assemblies, the votes for merger were greeted by roars of applause, cheers, whistles and singing. The Rev. Pat McGeachy of Nashville told fellow commissioners to the southern church's assembly after the vote that "there are a number of us here who are descendants of the signers of the Acts of Secession" which separated southern churches from the main body of Presbyterianism. "I think our ancestors would approve thoroughly" of the reunion vote.

The long-awaited reunion still leaves seven small Presbyterian denominations in this country--only one has as many as 100,000 members--that over the years split off from the mainstream of Presbyterianism, usually over differences in theology.

Young told the hymn-singing, dancing crowd of more than 7,000 gathered in the bright sunshine outside City Hall that "God has truly blessed this occasion."

Young, an ordained minister in the United Church of Christ and a favorite of church groups, said, "We share in the joy of your unity and pray that it might be extended from our nation to all other nations over the earth, that we all might live together as brothers and sisters."

The merger votes were expected. Both assemblies, after years of on-again, off-again negotiations, overwhelmingly approved the plan of reunion a year ago. Regional presbyteries of both churches affirmed that action in individual votes earlier this year.

Denominational officials expect that perhaps 40 of the southern church's 8,975 congregations may withdraw as a result of the merger.

The split in American Presbyterianism occurred in 1861, when the country was engulfed in civil war. The southern churches were asked to pledge "unabated loyalty" to the federal government. They refused and formed the Presbyterian Church in the Confederate States of America.

No serious efforts at reunion occurred until 1937, when the church formally voted to study the matter.

The reunion almost occurred in 1954, when national assemblies of both churches formally approved a plan. But the Supreme Court's landmark school desegregation decision that year reignited the old volatile mix of race and theology, and regional presbyters of the southern church voted down the proposal.

Today the two churches are more alike than they are different. Both are rated liberal on most social and political issues, though the northern church tends to be the more aggressive.

Both have played leading roles in providing money, leadership and enthusiasm to the ecumenical movement at local, national and world levels.

In terms of social status, both churches draw their membership largely from middle and upper-middle classes. Except in mission churches, there are not a lot of blue-collar Presbyterians, north or south.

Both churches are racially integrated and have pressed programs of affirmative action both in their own structures and in society at large. The northern church has 6 to 8 percent non-white members--blacks, Hispanics and orientals--and the southern church slightly less.

Both ordain women, but the United Presbyterians have been more aggressive in requiring local congregations to include lay women in equal numbers with lay men in leadership posts.

The three Protestant denominations with more members than the Presbyterian Church (U.S.A.) are the Southern Baptists, the United Methodists and the mainly black National Baptists.