His left-wing rival, Gustavo Petro, of the Humane Colombia movement, finished in second place, with 41.81 percent.
Duque will take over the presidency in August from outgoing President Juan Manuel Santos, whose term was marked by a peace deal with the FARC guerrilla group.
Most of the country backed Duque's business-friendly project, appealing to international investors that Colombia was open for trade and investment after years of violence. Petro, a former guerrilla and mayor of Bogota, campaigned on a more social project, vowing to tackle inequality.
While Petro won in his fiefdom of Bogota, the rest of Colombia's major cities sided with Duque, with Medellin, Cali, Bucaramanga and Cartagena all voting for Duque.
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