"My first priority will be recovering our economy," Yudhoyono, a former army general told reporters at his home on Wednesday as a stream of polls appeared to point the way to his victory.
"I just want to say how grateful I am to God Almighty, a big thank you to all my fellow colleagues, and my gratitude to all Indonesians that have cast their vote during today's presidential election" he said in televised comments.
Yudhoyono's rivals have been cautious about conceding defeat, with opponents hinting at the possibility of electoral fraud and questioning the validity of quick count polling.
"The current attempt to create perception that one candidate has practically won the election is completely wrong and we appeal to all sides to refrain from making such claims," Prabowo Subianto, Megawati's vice presidential running mate, told reporters ahead of the election commission's announcement.
The possibility of a challenge to the final result has raised fears of political deadlock in the wake of the vote.
Wednesday's election was only Indonesia's second direct presidential ballot and has been seen as a test of the country's young democracy.
There were no reports of major incidents or unrest at the roughly 450,000 polling stations set up across the sprawling archipelago.
More than 170 million Indonesians were eligible to vote, although the election commission has yet to release figures on the actual turnout.
The vote was a three horse race pitting Yudhoyono against Sukarnoputri, a former president whose father was the first post-colonial leader of Indonesia; and Kalla, Yudhoyono's current deputy who teamed up with Indonesia's former army chief Wiranto to mount a challenge for the presidency.
Just 10 years ago, Indonesia was labelled the "sick man of Asia", standing on the brink of political, social, and financial collapse after decades of entrenched corruption and nepotism under the former Suharto regime.
But observers say that Yudhoyono's government has brought political stability and peace to Indonesia and the best economic performance in a decade.
Yudhoyono's influence was strengthened in April's parliamentary election that saw his Democrat Party win about a quarter of the seats against only 7.5 per cent of the vote in 2004.
Despite the campaign promises, Indonesia continues to face huge obstacles on the path to democratic reform and many voters said they wanted candidates to make greater strides against corruption and widespread poverty - major challenges facing the predominantly Muslim country of 235 million.
With about 100 million Indonesians living on less than $2 a day, capturing the vote of the poor has been a priority throughout the campaign.