With 88.6 percent of votes counted, National Elections Commission chairwoman Frances Johnson-Morris said 59.2 percent of the vote was held by Ms Johnson-Sirleaf, while her opponent, George Weah, had 40.8 percent.
But Mr Weah, a former soccer star who was FIFA player of the year a decade ago, has claimed the vote was fraud.
Election officials said they would investigate fraud allegations from Mr Weah, who asked his supporters — including former warlords, rebel leaders and fighters — to remain calm while investigations are underway.
Ms Johnson-Morris told reporters the commission had received a formal fraud complaint from Mr Weah’s campaign, but she gave no details.
“We’ll do everything to expedite the investigation into this complaint,” she said.
International observers who monitored the poll said preliminary findings indicated it was fair.
Mr Weah accuses poll workers of having plans to stuff ballot boxes in Ms Johnson-Sirleaf’s favour, charges her campaign denied.
“It’s all lies. They’re saying that because they know we will win,” said Jemima Caulcrick, a top official of the Unity Party.
“They just don’t want a woman to be president in Africa. But she shall be.”
Mr Weah has accused the National Elections Commission of bias and called on Ms Johnson-Morris to step down.
He held talks with Alan Doss, head of the 15,000-strong peacekeeping mission deployed in Liberia since civil war ended in 2003.
“We are seeking the advice of the international community and all the people that are involved to see if everybody can arrest this situation,” Mr Weah said.
“While we are preparing ourselves for the legal side, we are also asking our people to be very calm.”
Mr Doss said the allegations of fraud are being taken seriously.
“Any allegation of any fraud is serious and we don’t want allegations of fraud to mar the election,” he said.
“These claims have to be taken seriously and looked into and followed-up immediately.”
Across the country’s bombed-out capital, large groups of excited Liberians stood listened to results as they were announced on radio.
Max van den Berg, head of a 50-member European Union observer mission, said the vote “has been well administered in a peaceful, transparent and orderly manner”.
David Carroll, leading a 28-person team from the Atlanta, Georgia-based Carter Centre, said that while “minor irregularities” had been noted, “none of our observers saw any serious problems”.
Observers from the Economic Community of West African States, which played a key role brokering peace in Liberia in 2003, also deemed the vote fair.
Ms Johnson-Sirleaf has a masters degree in public administration from Harvard University, and has held top regional jobs at the World Bank, the United Nations and within government.
Her supporters call her the “Iron Lady”, borrowing the nickname of former British prime minister Margaret Thatcher.
In elections in 1997, she ran second to warlord-turned-president Charles Taylor, who many claimed was voted into power by a fearful electorate.
Mr Taylor was forced out of power two years ago and now lives in exile in Nigeria.
Mr Weah and Ms Johnson-Sirleaf finished first and second in the October 11 first round.
Mr Weah’s ascent from Monrovia’s slums to international soccer stardom earned him popular appeal at home.