Sirisena, a former government minister who later changed sides to become the opposition's candidate in November, has vowed to root out corruption and bring constitutional reforms to weaken the power of the presidency.
Rajapaksa won handsomely in the last election in 2010, surfing a wave of popularity that sprang from the defeat in the previous year of ethnic Tamil separatists who had waged a war against the state for decades
Earlier results showed Rajapaksa remained popular among the country's Sinhala Buddhists, who account for around 70% of the population, but his challenger had taken a strong lead from the ethnic Tamil-dominated former war zone in the north of the country and Muslims-dominated areas.