In the cumulative results, officially declared at 2 am (local time), 63-year-old Sirisena took a slight lead by polling 1,87,615 votes as opposed to 69-year-old Rajapaksa's 1,43,415.
The results of only two polling divisions have been declared.
In Kilinochchi in the Tamil northern province, Sirisena won with 72 per cent of the votes as opposed to Rajapaksa's 24 per cent.
However, in the postal vote results declared so far, Sirisena has won only three of the 11 districts.
He won in his own Polonnaruwa district and two other districts in the north and east while Rajapaksa grabbed the Sinhala majority districts' postal votes.
Analysts say a photo finish is in the offing for the final victory.
Rajapaksa called early poll to seek his record third term and came up with an unexpected tough challenge from Sirisena.
There are 19 candidates in the fray. But the main fight is between two-term president Rajapaksa and his former cabinet colleague Sirisena.
