Results are expected in a few days.
The delayed vote on Tuesday pitted George Weah, a 51-year-old ex-international football star and Liberian senator, against 73-year-old Joseph Boakai, who has been the country’s vice president for the last 12 years.
Nearly 2.2 million people were eligible to vote in the runoff in the West African country.
Weah, who topped the first round of voting but did not secure the 50 percent needed to win outright, is heavily favoured to win the runoff.
“Vote counting is going on in polling stations across the country,” said Al Jazeera’s Mohammed Adow, reporting from the capital Monrovia.
“The electoral commission has two weeks to declare the results, but officials say they will do so within four days.”
Turnout was “nowhere near that of the first round held in October”, our correspondent said, attributing the low numbers to a seven-week delay in holding the runoff.
Initially scheduled for November 7, the vote was delayed after the party of a third candidate filed a legal complaint alleging voter fraud and irregularities.
Both Weah, the candidate for the Congress for Democratic Change (CDC), and Boakai, of the Unity Party, have promised to revive Liberia’s struggling economy and kick-start infrastructure projects.
Liberians are choosing a successor to President Ellen Johnson Sirleaf, Africa’s first elected female head of state, whose 12-year rule helped cement peace in Liberia after two bloody civil wars, which spanned 14 years before ending in 2003.
Henry Boyd Flomo, a spokesman for the National Elections Commission of Liberia, called the election “significant” and “historic”.
“It’s historic, because for many years, we haven’t had a sitting president willingly, democratically turn over to another person,” Flomo told Al Jazeera earlier in the day.
“And it’s the third consecutive election since the civil war. So it’s quite important, and we take it very seriously.
“What we hope is that the candidates respect the views of the voters.”
Boakai and Weah, after casting their ballots in Monrovia, both said they were confident of victory.
“This is a great day because it is a test of democracy,” Boakai said.
“We’re going to win because the people believe in us and they know we represent the best.”
Weah, who was defeated by Sirleaf in 2005, was certain that his second run for the presidency would be successful.
“Victory is certain. I am sure that I am going to win,” he said.
Alex Vines, head of the Africa Programme at the Chatham House, said Weah, who is seen as anti-establishment, was most likely to gain the upper hand in the runoff.
“This is because of a simple fact,” he told Al Jazeera from London.
“The majority of the Liberian population, 70 percent of it, is under 35. And he’s garnering the youth votes very significantly.
“So I think it will be George Weah as president.”
Observers, however, are worried that the losing candidate may contest the results, he said, adding: “It’s important for Liberia that the [losing candidate] doesn’t go for a perpetual challenge through the courts.”
The eventual winner faces a tough road ahead, analysts say.
Adama Gaye, a former official at the West African body ECOWAS, said the country’s new leader will have to deal with “a very difficult situation” in the wake of the Ebola crisis in Liberia, which killed thousands between 2014 and 2016, as well as a drop in commodity prices for the country’s main exports of rubber and iron ore.
He praised Sirleaf for her work, but said the country “has not been making progress on jobs, unemployment and attracting investment the country needs for infrastructure”.
Miatta Fahnbulleh, a musician and activist, said she hoped the more “tolerant party wins” Tuesday’s election.
Liberians are “waiting with bated breath” for the results, she said, adding: “If the wrong loser loses, we may not have peace for a while.”