Almost 2.2 million voters were choosing between the 51-year-old Weah and 73-year-old Vice President Joseph Boakai.
The run-off vote was delayed for over a month after Boakai and third-placed Charles Brumskine of the Liberty Party alleged widespread fraud in October's first-round vote, a challenge that the Supreme Court rejected this month.
The former football star's campaign - under the Coalition for Democratic Change banner - appealed to the youth vote, while incumbent Vice President Mr Boakai was seen as old and out of touch.
The ex-footballer, who played for AC Milan, Manchester City, Chelsea and Paris Saint-Germain during his career, leads the presidential run-off with 61.5% of the vote with 98.1% of ballots counted, the commission said. That triggered a run-off as neither made it past the 50 percent needed to win outright.
Victoria Blamoh (56) told AFP she voted for Boakai's "experience of leadership", explaining: "He has been in government for 12 years, so he knows the ins and outs of it".
The nation has been dogged by civil war and heavy-handed rule throughout its history.
Living standards in Liberia remain among the worst in the world.
Football great George Weah has reportedly been elected the new President of Liberia after nationwide polls on Boxing Day.
But Mr Weah's election is not without controversy, as his running mate is Jewel Taylor, former wife of the warlord and ex-President Charles Taylor, who is serving a jail sentence in the United Kingdom for war crimes.
He said "the emergence of George Weah as Liberia President 12 years after he was short-changed by those who wielded power at that time is a further confirmation that that there is no God in man".
On Tuesday polling stations displayed voter lists as a mark of transparency.