In contrast to the long queues which formed outside polling stations in the first round, few people were voting in the capital Monrovia.
Incumbent president and joint Nobel Peace Prize laureate Ellen Johnson Sirleaf won the first round with Winston Tubman, a former UN diplomat, in second place.
Ahead of Tuesday’s vote Tubman urged his supporters not to vote in the second round claiming the process was fraudulent.
His call for a boycott has drawn wide international condemnation, and raised fears for the legitimacy of an election billed a litmus test of the nation's fragile democracy and hard-won peace.
Shooting erupted on Monday as tensions soared between anti-riot police, UN peacekeepers and thousands of protesters gathering for an unauthorised march called by Tubman a day after the official end of campaigning.
Some 1.8 million voters have registered for the election. Despite his boycott, Tubman will still appear on the ballot paper.
Sirleaf, who made history when she became Africa's first elected female president in 2005 and jointly won the Nobel Peace Prize shortly before the first round, has accused her rival of violating the constitution.