But monitoring groups said the election was flawed by flagrant violations.
Mrs. Kumaratunga won 51.12 percent of the vote, ahead of her nearest challenger, Ranil Wickremesinghe, who garnered 42.7 percent, the Election Commission announced.
The result denied Mrs. Kumaratunga the sweeping mandate she sought when she called the election 11 months earlier than scheduled, and was far less than the landslide 62 percent she won in 1994.
Many voters apparently were disappointed that she had failed to fulfill her promise to end the war with the Tamil Tiger separatists, which has instead grown progressively more fierce.
An assassination attempt against her on Saturday, when a suspected Tamil rebel blew herself up with explosives strapped to her body, appeared to have had little effect on the vote.
Mrs. Kumaratunga was injured by the bomb, and did not leave her home Tuesday to cast her ballot. The ballot box was instead flown from her home district to her official residence.
The Commission said 73 percent of the 11.7 million voters cast ballots, despite threats from Tamil rebels to disrupt the voting.
The independent Center for Monitoring Election Violence said the poll was marred by serious election violations, systematic impersonations and ballot-stuffing.
"The result of this election has been irredeemably compromised," said the organization's director, Paikiyasothy Saravanamuttu.
Because of irregularities, the monitors said the election should be nullified in the entire northeast region and polling should be held again. The northeast is the Tamil-dominated area where the rebels want to carve out an independent Tamil state.
Together with other districts, the monitoring center said, "for over one-third of the country, the 1999 presidential election was a less than satisfactory exercise in democracy."
Another monitor, Kingsley Rodrigo, said the center had received more than 350 complaints of election violations.
At least seven people died in election violence.
Authorities removed a nighttime curfew Wednesday that was imposed across the country to prevent further violence between rival political or ethnic groups.
In scattered election violence, three men believed to have been supporters of Mrs. Kumaratunga died when unidentified attackers threw hand grenades at them near the town of Dumbalasuriya, 40 miles north of Colombo. Another man died in the same area, and one was seriously wounded in a confrontation with police. Three more bodies were recovered across the country.
A total of 11 candidates are in the race, but the real contest was between Mrs. Kumaratunga and Wickremesinghe, who has rejected the president's approach of militarily crushing the separatist rebels if thy don't surrender their weapons and return to the negotiating table.
The rebels are waging a war for an independent homeland for the country's minority Tamils. An estimated 61,000 people have died in the 16-year insurrection and 1.2 million have been made homeless on the island off India's southeast coast.
Tamils have a language, religion and culture distinct from that of the Sinhalese. The two groups have periodically fought over territory for 1,000 years.
Wickremesinghe has said he would abandon the military option and open unconditional peace talks with the rebels, although he has not said what peace proposals he would offer them.
Mrs. Kumaratunga has drawn up a constitutional reform package extending autonomy to the provinces, including the Tamil-dominated areas, in hopes of satisfying moderate Tamils.
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