He is now likely to face off against leftist former rebel Gustavo Petro, who had the seemingly-unsurmountable edge in a tight race for second place.
With almost all polling stations reporting, Duque won 39 per cent. He was trailed by Petro, who won 25 per cent, and former Medellin Mayor Sergio Fajardo, who finished with 24 per cent and had not yet conceded defeat.
With 53 per cent of registered voters casting ballots, turnout was highest in two decades.
The two presidential candidates represent opposite ends of Colombia's political spectrum and have presented dramatically different visions for the future of the Andean nation as it moves forward with a historic peace process with leftist rebels.
Duque is the hand-picked candidate of Alvaro Uribe, the former president and chief critic of the nation's 2016 peace deal with the Revolutionary Armed Forces of Colombia.
He is promising to amend important aspects of the accord like ensuring the drug trafficking is not an amnestied crime.
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