GUATEMALA CITY, NOV. 12 -- An evangelical Christian who ran a low-budget campaign and barely registered in the polls until this fall stunned Guatemala's political establishment today with a strong showing in the still incomplete count of Sunday's presidential election.

With three-quarters of the vote counted, Jorge Serrano Elias, 45, who served under a past military ruler, was in a virtual tie with Jorge Carpio, 58, a newspaper publisher who has spent heavily in a five-year presidential campaign.

Serrano, an engineer and educator, became the instant favorite to win the Jan. 6 runoff, in part because of the electoral strength of Guatemala's Protestant evangelicals. They comprise about a third of the population. He also is considered likely to collect the votes of Alvaro Arzu, a former mayor of Guatemala City who was running third and who is a rival of Carpio.

So confident was Serrano of winning the runoff that he said he would name a presidential transition team today. "This is an earthquake," he said.

Political analysts agreed. Said the newspaper La Hora: "Serrano's stunning showing has turned the political landscape of the country on its head."

For much of this year, a former military dictator, retired Gen. Efrain Rios Montt, was believed to be the front-runner in the presidential elections. An evangelical who gave televised Sunday sermons during his brief, violent, coup-bracketed presidency in 1982-83, Rios Montt billed himself as a law-and-order candidate who offered a return to what he called traditional values.

However, Rios Montt was disqualified last month by the courts, which cited a constitutional ban on candidates who previously held power as the result of a coup.

Soon after, Serrano, the only other evangelical conservative in the race, surged in the polls, apparently picking up some of Rios Montt's supporters. There was another link between the two: During his presidency, in which thousands of Indians were killed in a counterinsurgency campaign in the countryside, Rios Montt appointed Serrano as head of the council of state, a nonconstitutional legislative body.

Nevertheless, Rios Montt did not endorse Serrano but asked his followers to negate their ballots. Only a small number of spoiled ballots have been registered.

Several analysts said today that even though Serrano has not emphasized his religion during the campaign, it would probably help him in the runoff. "There's a significant portion of the evangelical population that will rally behind him, even though the Protestant community here is not a disciplined and well-organized base," said Dennis Smith, who works for an evangelical study center here.

While evangelism has made steady gains throughout Central America during the past decade, its greatest gains have been in Guatemala. Much of its success has come at the expense of the Roman Catholic Church, which has dominated religious life in the region since the Spanish conquest.

By stressing an individual's relationship with God and salvation in the kingdom of heaven, evangelicals have made inroads, particularly among the poor. They have also been helped by contributions from evangelical churches in the United States, which have supported active missions in Central America.

Catholic Church officials have criticized evangelicals for encouraging the downtrodden to accept injustice and poverty on Earth passively, in return for the promise of redemption in heaven.

Some worried today that the runoff would be marred by religious recriminations. "I do not rule it out that somebody -- the Catholic Church -- will bring it up," said Claudio Riedel, a foreign policy adviser to Carpio.

Sunday's elections marked a political watershed for Guatemala: the first elections in decades to choose one civilian president to succeed another. The Central American country of 9 million people saw a series of military dictatorships until 1986, when President Vinicio Cerezo was elected.

Cerezo assumed office with overwhelming popular support, but his rule provoked two coup attempts, allegations of corruption and constant rumors about his womanizing.

His handpicked successor in the Christian Democratic Party, Alfonso Cabrera, was running a distant fourth in Sunday's election.

So new is civilian rule in Guatemala, where two out of three people are illiterate, that many people equated Cerezo with democracy itself. His fall from grace was reflected by polls that also showed many Guatemalans were disillusioned with democracy and thought military dictators were better at running the country.

The disillusionment was reflected by a turnout of about 57 percent of the 3.2 million eligible voters. Although the elections were peaceful, many people said they could not name the candidates and were doubtful any could make a difference.