On Monday huge crowds watched the funeral motorcade make its way to the Suharto mausoleum, many weeping and waving flowers.
During the funeral ceremony, after a long reading of Suharto's military accomplishments, a shot was fired in his honour and Yudhoyono saluted the former leader.
"We offer his body to the motherland," the Indonesian president said. "His service is an example to us."
Earlier Suharto's body was held overnight at his villa in the capital, Jakarta, before his flag-draped coffin was driven by military escort to an Indonesian air force base on the outskirts of the city for the short flight to Solo.
Announcing Suharto's death on Sunday, Yudhoyono declared a week of national mourning.
"I invite all the people of Indonesia to pray that may the deceased's good deeds and dedication to the nation be accepted by Allah the almighty," he said in a televised address.
Agung Laksono, the speaker of the Indonesian House of Representatives, called on Indonesians to pray for Suharto's soul "that his sins be pardoned and his good deeds be received."
Indonesia's Antara news agency said that two tonnes of jasmine flowers and 100 kilos of roses had been prepared for the funeral ceremony.
Suharto's condition had fluctuated since being admitted to hospital more than three weeks ago with doctors at one point saying he was making an "amazing recovery".
He was forced to stand down in 1998 amid widespread protests triggered by the impact of the Asian financial crisis.
|Suharto's eldest daughter called for |
forgiveness for her father's "faults" [AFP]
He was accused of siphoning off billions of dollars in state funds into his own secret bank accounts, but his lawyers successfully argued that he was too ill to stand trial.
According to one study, by corruption watchdog Transparency International, Suharto and his family embezzled up to $35bn during his 32 years in power.
He was also accused of presiding over some of the bloodiest episodes in post-second world war Asia, including the crushing of the Indonesian communist party in the mid-1960s, and the invasion and occupation of East Timor a decade later.
Both incidents led to the deaths of hundreds of thousands of people.
Speaking shortly after his death on Sunday, Suharto's eldest daughter, Siti Hariyanti "Tutut" Rukama, called for forgiveness for her father.
"Father has returned to God," she said, speaking outside the central Jakarta hospital where he had been treated for the past three weeks.
"We ask that if he had any faults, please forgive them ... may he be absolved of all his mistakes."