More than 121 million votes were counted, but the commission gave no official figures for the number of invalid ballots or voter turnout.
The president's victory means he will avoid having to campaign in a second-round vote in the midst of a nationwide security alert following two deadly bomb attacks on hotels in the capital, Jakarta, last week.
Yudhoyono had been praised with bringing Indonesia record economic growth and restoring security after a series of high profile attacks, including the 2002 Bali bombings which killed 202 people.
But the Jakarta blasts have come as a reminder that Indonesia's crackdown on militant violence may not have been as successful as many had thought.
The July 8 election was only Indonesia's second direct presidential ballot and was seen as a key step towards cementing the country's young democracy.
The election campaign and vote passed off largely peacefully and was praised by outsiders as free and fair.
Yudhoyono's rivals however have accused his party of electoral fraud and said in the days after the election that they planned to formally contest the outcome.