An unusually high voter turnout was witnessed in Tamil and Muslim-dominated areas, as the election officials estimated more than 65-70 per cent voting in most places.
There were no major reports of violence, although private monitoring group the Campaign for Free and Fair Elections (CaFFE) said some voters had been prevented from voting that ended at 4 pm local time.
Over 15.4 million of the country's 21 million population are eligible to vote. About 1,076 polling stations were set up for elections.
There are 19 candidates in the fray. But the main fight is between two-term president 69-year-old Rajapaksa and his 63-year-old former cabinet colleague Sirisena.
Long queues were seen outside the polling stations around the country.
"There is heavy polling everywhere," Keerthi Tennakoon of Campaign for Free and Fair Elections (CAFFE) said.
Rajapaksa said he was confident he would return to power as he cast his ballot.
Main opposition candidate Sirisena, who has vowed to root out corruption and political decay, said: "My victory is in sight. There is support for us everywhere."
Voters from minority Tamil community turned out to vote in large numbers in the areas dominated by them, defying intimidation attempts.
In the three northern districts of Tamil regions in Jaffna, Kilinochchi and Mullaithivu over 50 per cent polling was recorded.
In some Muslim dominated areas, mosques' loudspeakers were used by the community members to encourage voters to cast their votes.
"People are keen to vote, there were several hundreds already queueing up when the poll stations opened," said E Saravanabhavan, a Tamil parliamentarian from Tamil National Alliance (TNA).
