It was not immediately clear who Yudhoyono would face in a second round, with President Megawati Sukarnoputri and another ex-army general, Wiranto, locked in a tight race for second place.
The outcome was further in doubt after tens of thousands of ballots cast in Indonesia's first direct presidential election will have to be recounted because voters inadvertently spoiled them, election officials said Monday.
Hamid Awaluddin, an election commission member, said the problem could affect "millions" of the total vote count of 140 million. But he said the process would not significantly delay the count, which could take up to a week.
"It's not a major obstacle," he said. "We can safely say that the elections went well."
Officials became aware of the problem when some polling stations reported high numbers of spoiled ballot papers, apparently caused by voters punching the paper when it was folded in two.
Elections officials ordered the stations to count the votes as valid. Out of the some 2 million votes counted late Monday, just under 3 percent were initially ruled invalid, according to the election commission's Web site.
Polls have shown Megawati - daughter of the country's founding father, Sukarno - trailing Yudhoyono, a former security minister who resigned from her Cabinet months ago to seek her job.
But the surveys also have suggested no candidate would get more than 50 percent of the vote, meaning there would be a runoff between the two top vote-getters in September.
The election in the world's largest Muslim nation was a massive enterprise, with more than 155 million eligible voters spread across 13,000 islands and three time zones. Previously, presidents were selected by lawmakers acting as an electoral college.
"This is a wonderful transitional from authoritarian rule to pure democratic rule," said former President Jimmy Carter, who was observing the vote in Jakarta. "We have been greatly impressed by the orderly and well-planned procedures taking place this morning."
Election officials reported that balloting was peaceful and largely free of problems. But they said the voting got a slow start in the capital where many soccer fans were sleeping in after staying up overnight to watch the European championship match.
Endah Sari, a housewife in Jayapura, capital of the eastern province of Papua, where polls opened first -- was among the first to vote Monday.
"As a citizen of Indonesia, I want to use my right to pick the president because this is important for all of us," said Endah Sari, a housewife in Jayapura, the capital of Papua, as she cast her ballot.
In Jakarta, voters said the election gave them a greater voice in running the country.
"This makes me feel like the freedom is real," said Budi Supriadi, a 40-year-old fish salesman. "This is a first step toward a better future."
Yudhoyono said he was confident of at least getting into a run-off, so long as there are no widespread voting irregularities.
"I have traveled the country and seen the people's support for me," Yudhoyono said.
Dozens of voters bent and kissed Yudhoyono's hand as he left the voting booth.
"We're suffering," said Mistar, a 40-year-old garbage collector who raises three children on a salary of $3 a day. "Yudhoyono seems like a credible man who will listen to us. I don't think Megawati cares."
Megawati emerged as the country's most popular politician in the tumultuous days following the ouster in 1998 of Suharto, who had ruled Indonesia since overthrowing her father Sukarno in 1966. Her party won more than a third of the vote in free elections in 1999.
But in the past five years, Megawati's popularity waned because of her failure to combat corruption or improve the economy, and a perception that she is aloof and indifferent to the concerns of the people.
In contrast, ex-army general Yudhoyono is a polished operator who projects stability and reassurance.
Megawati said nothing to reporters Monday, but held up an inky finger ? a method used here to ensure that people only vote once ? to supporters at her home in an upscale Jakarta neighborhood.
Three other candidates are also running, including Wiranto, a former commander of the armed forces indicted by U.N. prosecutors in East Timor for crimes against humanity allegedly committed in that former Indonesian province in 1999.
Wiranto, though tainted by the U.N indictment, has secured the support of the country's largest party.
Pre-election surveys showed Yudhoyono leading with about 40 percent of the vote. Neither Megawati nor any other contender had more than 15 percent, and a fifth of voters were undecided.
The run-up to the election was orderly, with none of the protests, violence or investor jitters that have characterized political conflicts and rivalries in recent years.
By Slobodan Lekic