Mr Yudhoyono is now favourite to win
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Indonesia will hold a run-off poll for president in September after the first round did not produce a clear winner.
Results from the 7 July poll, announced on Monday, gave former general Susilo Bambang Yudhoyono the most support.
He will now contest the run-off with incumbent Megawati Sukarnoputri, who narrowly beat another former army chief, General Wiranto.
The election results were delayed for a few hours after a small explosion at Jakarta's election commission.
The city's police chief said a small bomb had caused the blast, but no one is thought to have been injured.
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OFFICIAL RESULTS
Susilo Bambang Yudhoyono - 33.5%
Megawati Sukarnoputri - 26.6%
Gen Wiranto - 22.2%
Amien Rais - 14.7%
Hamzah Haz - 3%
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The 5 July elections marked the first time that Indonesians had the chance to vote directly for their president.
Mr Yudhoyono came out in first position with 33.5% of votes cast.
But he failed to get the 50% majority needed to avoid a run-off with the second ranking candidate.
In a tight race, Mrs Megawati polled 26.6% to come in second, ahead of Gen Wiranto's 22.2%.
International election observers, including former US President Jimmy Carter, judged the poll as largely free and fair.
Despite this, Gen Wiranto - the candidate backed by the Golkar party, which topped the April legislative elections - has accused the other candidates of electoral fraud.
Last week he said he intended to challenge the validity of the election in court, but analysts say he has little chance
of winning a case.
Narrow fight
Fresh from his first round victory, Mr Yudhoyono is the favourite to win the second round on 20 September, and become Indonesia's next president.
The race could be close though, especially if Mrs Megawati wins the support of Golkar voters.
Over the next two months, both candidates are likely to gather support from other parties by offering them cabinet seats in exchange for votes.
Just before an official announcement of the results was due, a small bomb exploded in a women's toilet inside the election commission's offices in central Jakarta.
Workers inside the building had reportedly just stopped work for prayers when the blast occurred.
"The damage was small so I think it came from a low explosive. All we can say is, it was like a firecracker," Jakarta's police chief Firman Gani told reporters.
"I don't see this incident will disturb the process of the
election," Mr Yudhoyono told reporters after hearing about the blast.