A former cabinet colleague of Rajapaksa and General Secretary of the Sri Lanka Freedom Party, 63-year-old Sirisena was leading with about 56 per cent of the nearly 600,000 votes counted so far, with Rajapaksa trailing at 41 per cent.
About 75 per cent of the 15.04 million electorate voted in election called two years ahead of schedule by Rajapaksa who was confident of securing a record third term.
Sirisena took strong lead from the ethnic Tamil-dominated and Muslims-dominated areas.
Hailing from the rural north central province, Sirisena does not speak English, is ever seen in the national dress.
He has no background of hobnobbing with the Colombo elite and socialites. No old boy of a leading Colombo school, he was more than a match for Rajapaksa's rural appeal.
69-year-old Rajapaksa left his official residence this morning, with cumulative results showing Sirisena ahead.
"President Rajapaksa left Temple Trees bowing to the people's mandate in the presidential election", a statement from the President's office said.
There was no immediate comment from Sirisena, who was still at his private home in Polonnaruwa, 215 kilometres east of the capital Colombo.
There were 19 candidates in the fray. But the main fight was between two-term president Rajapaksa and Sirisena.
Of the 160 poling divisions, results for 19 poling divisions have been announced. Rajapaksa has won only six.
Rajapaksa, who has been accused of running a family rule and turning the country into an authoritarian regime, will be regretting for calling the snap poll two years ahead of schedule.
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