About 13,4 million of South Korean nationals participated in the election, the NEC added, as cited by the Yonhap news agency.
A total of 13 hopefuls took part in the presidential race after two nominees had dropped out. Moon Jae-in of the liberal Democratic Party of Korea was considered as one of two main rivals along with and Ahn Cheol-soo of the center-left People's Party.
The vote took place less than two months after President Park Geun-hye was ousted following a corruption scandal that also led to her arrest.
The new president of South Korea will take office on May 10, immediately after the confirmation of the results by the NEC.