"President Rajapaksa left Temple Trees bowing to the people's mandate in the presidential election", a statement from Rajapaksa's office said.
With final result yet to be declared, Sirisena is expected to be declared winner by around 4,00,000 votes.
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Rajapaksa, who sought a record third term, was involved in a grim battle for survival.
Sri Lankans yesterday voted in large numbers in the bitterly contested presidential election in the biggest political shake-up in over a decade. The election officials had estimated more than 65-70% voting in most places.
There were 19 candidates in the fray. But the main fight was between two-term president 69-year-old Rajapaksa and his 63-year-old former cabinet colleague Sirisena.
Rajapaksa had called the election two years ahead of schedule, hoping to win a record third six-year term before the defeat of the Tamil Tigers fades in the memory of the people of the island which saw a three decades war over the demand of a separate Tamil Eelam.
The veteran politician was taken by surprise by the candidacy of former health minister Sirisena, who walked out of the government a day after polls were called. That set off a wave of political turmoil and energised a long-dispirited opposition that had not been looking forward to the election.
Rajapaksa was the undisputed leader of Lanka for nearly a decade. But the country is grappling with divisions between the Sinhalese majority and Tamil minority groups.
The opposition campaign had accused Rajapaksa of nepotism, misrule, corruption and authoritarianism.
Rajapaksa's brothers - Gotabhaya and Basil - are defence and economic ministers respectively besides a number of his family members who are holding key posts and positions.
Sirisena backed by the main opposition United National Party and another key breakaway group the JHU or the Buddhist Monk party have plans for a series of constitutional and democratic reforms.
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