Polls opened around the country at 8 am (1300 GMT) and were to close at 4 pm (2100 GMT), election officials said.
Voters will choose between President Juan Manuel Santos, who is seeking a second term, and Oscar Ivan Zuluaga, a vehement critic of the president's peace talks with the Revolutionary Armed Forces of Colombia (FARC).
Santos, 62, cast his ballot shortly after polls opened, with Colombians still euphoric over their national team's 3-0 World Cup victory yesterday over Greece.
The bid to end Latin America's longest guerrilla war has emerged as the central issue of the run-off elections with Colombians torn between the hopes and fears aroused by a mudslinging campaign.
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Zuluaga, 55, has long been opposed to the peace talks but now says that he would negotiate with the rebels under stricter conditions.
Santos argues that Colombians must choose between "the end of the conflict or an endless conflict."
The internal war, with its violent cocktail of rebels, paramilitary militia and criminal gangs, has left more than 220,000 people dead and forced five million people to leave their homes over the past half century.
A runoff was necessary since neither won more than 50 per cent of the vote, and pre-election surveys show no clear winner.
Both Santos and Zuluaga were cabinet ministers under the hard-line former president Alvaro Uribe who served from 2002 to 2010 and remains a powerful political force.
Santos was Uribe's defense minister, known for an aggressive military campaign that mauled the FARC and killed key rebel leaders.
But Uribe -- who is also a senator-elect -- threw his weight behind Zuluaga, his former finance minister, even calling Santos a traitor for negotiating with the rebels.