"We must be ready to face the challenges of reaching new heights after this vote," the 64-year-old, who called the election only four years into his six-year term to seize on the government's victory over the Liberation Tigers of Tamil Eelam (LTTE) last year, said.
Fonseka, however, suffered the embarrassment of not being able to vote, a problem he blamed on his name being omitted from the 2008 electoral register which was used for the poll.
"My name is not on the 2008 register and therefore I cannot vote at this election," Fonseka said.
"The government is trying to use this to mislead the public at the last minute."
The opposition figurehead insisted he had sent in his voter registration papers.
Ruling party politicians appeared on television saying he might be disqualified.
"We are seeking a court order on the suitability of this candidate because he is not eligible to be declared as a candidate," Rohitha Bogollagama, the foreign minister, said.
However, Fonseka received the full backing from the independent elections commissioner who said he was still eligible for the presidency.
Dayananda Dissanayake, the independent Elections Commissioner, said: "Not having one's name on the electoral list is not a disqualification."
Polling was reported to be busy in many areas, with people in the suburbs of the capital Colombo lining up half an hour before polls opened at 7am (01:30 GMT),
according to witnesses.
Last May, Rajapakse and Fonseka defeated the Tamil Tiger separatists, who had fought for a Tamil homeland since 1972, in a military campaign which has since been dogged by allegations of war crimes.
|Fonseka blamed the use of the country's 2008 register for not being able to vote [AFP]
But from close allies on the battlefield they have turned into irreconcilable enemies after Fonseka, a 59-year-old political newcomer, decided to challenge his former boss on an anti-corruption platform.
There are no reliable opinion polls in the country and political observers said the election was too close to call between the men, who were the only realistic contenders in a field of 22 people.
The Centre for Monitoring Election Violence (CMEV), an independent monitoring body, confirmed nearly 100 violent incidents during the day, mostly in northern and eastern areas, and said the figure could rise to 150.
Pre-dawn bomb blasts in the northern Tamil heartland of Jaffna gave a violent start to the contest which threatens to bring new instability to the Indian Ocean island nation.
Dissanayake, a CMEV national co-ordinator, said: "We can't say it was a free and fair election because there were a number of incidents all over the country.
Before the election, Fonseka had alleged the government would intimidate voters and was preparing a coup if it lost.
He was accused in turn of working with a militia of army deserters to disrupt the ballot.
In the Tamil-dominated town of Vavuniya, where CMEV said grenades were let off near a polling station, streams of people caught up in the war made their way to makeshift voting booths in schools.
Kandaswamy Wellarayanam, a Fonseka supporter, 73, walked six kilometres from one of the nearby internment camps where thousands of displaced Tamils were locked up after the fighting ended in May.
Now able to move freely after repeated condemnation of the camps by the United Nations, he said he and his family were eager to take part, even though buses that were meant to transport them never turned up.
"We walked to vote because we felt it was important after the war," he told the AFP news agency.
"I was keen to have a say in who should be our next president."
The opposition has said it would not accept the result if the 68,000 police and 12,000 soldiers on duty failed to prevent violence or if there was evidence of vote-rigging.
The alliance behind Fonseka, which includes Marxists, Muslims, Tamils and right-wingers has threatened to stage street protests if it feels the result has been stolen.