Final official results showed Yudhoyono and his running-mate Boediono with 60.8 percent of the vote, far ahead of ex-president Megawati Sukarnoputri with 26.8 percent and Vice President Jusuf Kalla with 12.4 percent.
The figures, which confirmed quick counts from independent pollsters, were released on the election commission's website and will be formally announced on Saturday.
Megawati and her running-mate, ex-general Prabowo Subianto, have complained of irregularities in the elections and threatened to mount a legal challenge to the results, as they did after poor performances in April's legislative vote.
The street outside the election commission has been blocked for the past two days with razor wire and armoured vehicles but there have been no signs of unrest.
Yudhoyono spokesman Andi Mallarangeng said any candidate had a right to contest the results but reminded Megawati and Kalla that they had signed an agreement to respect the outcome of the vote.
He said the president was willing to put aside their differences and work together for the country.
"Our priority for the next three months is to reconcile with all presidential candidates," he told AFP.
"There's time for competition and there's time to reunite to build our nation. We want to have good relationships with all presidential candidates."
Kalla's Golkar Party, the political vehicle of late dictator Suharto which which has never been in opposition, has shown signs it is willing to bury the hatchet and join a Yudhoyono-led governing coalition.
But Megawati, the daughter of late independence hero Sukarno, is bitterly opposed to the mild-mannered ex-general who defeated her by a massive margin in the 2004 polls and her campaign has said it will not sign off on the results.
Yudhoyono, 59, campaigned on a platform of clean government, decentralisation and pragmatic economic management in Southeast Asia's biggest economy.
Last week's terror attacks on luxury hotels in Jakarta, which killed seven people plus two suicide bombers, have shaken investor confidence but are unlikely on their own to change forecasts for robust economic growth.
The bombings were the worst terror attacks in the country since 2005 and have been blamed on Islamist extremists linked to the regional Jemaah Islamiyah network and Al-Qaeda.
Elite paramilitary police will ensure tight security at Saturday's result announcement in response to allegations by Yudhoyono that the bombings could be linked to efforts to overturn the election result, election commission spokesman Prasetyo Sudrajat said.
"We don't expect demonstrations, it's a bomb we are anticipating," Sudrajat said.
Sudrajat said they were unsure if Megawati's campaign would go through with threats to boycott the signing of the results but the Yudhoyono and Kalla camp had confirmed their attendance.
"The results will still be legitimate even if they don't sign - it's not obligatory."
The first five-year term of Yudhoyono, the first directly elected president in the mainly Muslim country of 234 million people, was marked by strong growth, political stability and the end of a separatist conflict in Aceh.

