With 99.93 per cent of ballots counted, Pinera on Sunday got 54.58 per cent of the vote against centre-left candidate Alejandro Guillier, who won 45.42 per cent, the poll body said.
Pinera, 69, was Chilean President between 2010 and 2014, Efe news reported.
Speaking alongside Guillier, Pinera struck a gracious tone on Sunday.
The President-elect said he had great appreciation and affection for Guillier.
He also said he had read Guillier's campaign programme very carefully and agreed with some of the ideas. Pinera added that they would discuss differences "with a republican spirit".
"Chile needs agreements more than clashes ... dialogue and collaboration, as that is how countries progress on solid foundations," Pinera said.
He admitted to having been surprised in both rounds of the election. Guillier has accepted his defeat and congratulated Pinera in his concession speech.