If legal challenges mounted by opposing candidates fail, Yudhoyono would be installed as president for a second, five-year term Oct 20.
More than 176 million people were registered as eligible voters but nearly 50 million of them did not vote, the commission said.
Yudhoyono, 59, has been credited with some successes in his first term, including stabilising the economy, cracking down on deep-rooted graft and bringing peace to the rebellious Aceh province.
Analysts said his resounding victory gives him a stronger mandate to pick professionals for his next cabinet and push through reforms as he faces the daunting task of tackling the effects of the global economic crisis.
Last week's bombings at two luxury hotels in Jakarta, which killed nine people including two suspected suicide bombers, have raised fears of a return of instability to the world's most populous Muslim nation after a few years of calm.
Police suspect the attacks were the work of Islamic extremists linked to Jemaah Islamiyah, a militant group that has been blamed for a string of previous deadly bombings in Indonesia.
Experts hailed this month's peaceful election as an indication of how Indonesia has come a long way since the turmoil that marked former dictator Suharto's departure in 1998.
A decade ago, South-East Asia's largest economy was a shambles, being hard hit by the region's 1997-98 financial crisis.
Until a few years ago, Indonesia still grappled with a separatist insurgency in Aceh and Muslim-Christian violence in the east of the country.