Wednesday's vote is Indonesia's second direct presidential election and is seen as an important step in cementing the country's democracy.
"Today is the people's day," Yudhoyono told reporters after casting his ballot in the town of Bogor on Java island.
Yudhoyono's main rivals both cast their votes in the capital, Jakarta, early on Wednesday.
In the former province of East Timor, now a nation in its own right, about 3,670 voters turned out.
Despite the poll predictions, Kalla told reporters he remained confident.
"Yes, we are feeling good and we are very optimistic" he said.
The election is a three horse race pitting Yudhoyono against Megawati, a former president whose father was the first post-colonial leader of Indonesia; and Kalla who has teamed up with General Wiranto, the former head of the armed forces during the Suharto era.
Indonesia continues to face huge obstacles on the path to democratic reform and voters will want their 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.
A controversy over voter lists marred the run-up to the vote with the teams of Yudhoyono's two rivals complaining about millions of duplicate names and even the names of dead people and children being on the electoral rolls.
Their complaints may have increased doubt about the credibility of the process, and could make it easier for the losers to challenge the result.
This week, the constitutional court sided with an opposition demand that other citizens, possibly numbering into the tens of millions, will be allowed to make last-minute registrations to exercise their right to vote.
The National Election Commission has been widely criticised for failing to compile a list of registered voters, as it did in the April elections.
Yudhoyono's rivals, while providing no proof, claim that millions of people will be unable to participate.
Megawati had warned supporters to beware of electoral fraud in the final weekend of campaigning in central Java.
"They think the people are stupid, can be manipulated, intimidated and terrorised," she was quoted as saying by the Kompas news website, repeating her claims that electoral officials are biased towards Yudhoyono.
Megawati, who leads the Democratic People's Party of Struggle, has a strong following as the daughter of independence hero Sukarno and was the figurehead of the opposition against Suharto's government in the late 1990s.
Under her presidency the administration was widely known for inaction and corruption and she was ousted in a 2004 landslide that brought Yudhoyono to office.
|Kalla, Yudhoyono's current deputy, has run a tough campaign against his boss [Reuters]
The "dark horse" in the race is Kalla who has trailed in opinion polls but has proven to be a tough competitor.
With his motto of "the faster, the better", Kalla and Wiranto have attacked Yudhoyono as a "neo-liberal" and championed a philosophy of economic "self-reliance".
Megawati also advocates a "people-centred economy" and her running mate, former special forces commander Prabowo Subianto, has openly compared his brand of economic nationalism to that of Hugo Chavez, the Venezuelan president.
By contrast, Yudhoyono has chosen Boediono, a Western-educated economist and former central bank governor, as his vice-presidential candidate.