With 88.6% of votes counted, the National Election Commission (NEC) said 59.2% of the vote was secured by 67-year old Ellen Johnson-Sirleaf.
George Weah, a one-time FIFA soccer player of the year, had 40.8% of the vote.
Election officials said on Thursday they would investigate allegations from the Weah camp of electoral fraud.
NEC Chairwoman Frances Johnson-Morris told reporters that the commission had received a formal fraud complaint from Weah's campaign, but she didn't release details.
"We'll do everything to expedite the investigation into this complaint," she said.
Late on Wednesday, Weah accused poll workers of having plans to stuff ballot boxes in Johnson-Sirleaf's favour.
"They just don't want a woman to be president in Africa. But she shall be"
Johnson-Sirleaf's Unity Party
Johnson-Sirleaf's team denied Weah's allegations.
"It's all lies. They're saying that because they know we will win," said Jemima Caulcrick, a top official of Johnson-Sirleaf's Unity Party.
"They just don't want a woman to be president in Africa. But she shall be."
Weah has repeatedly been critical of the National Election Commission and Johnson-Morris, who is not related to Johnson-Sirleaf.
International observers who monitored the poll said preliminary findings indicated it was fair.
UN officials and others have praised the vote.
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
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."
At the end of Tuesday's vote, Alan Doss, who heads the 15,000-strong UN peacekeeping mission, also said the vote had been transparent.
Weah and Johnson-Sirleaf finished first and second in the 11 October first round, which weeded out 20 other candidates, including warlords and rebel leaders.
Tuesday's run-off was held because no one won an outright majority in the first round.