Caputova, a lawyer by profession, defeated Maros Sefcovic, a candidate nominated by Slovakia's ruling party.
In the second round of voting held on Saturday, Caputova received 58.40 per cent of votes, while Sefcovic got 41.59 per cent of votes, Xinhua News Agency reported.
In the first round of polls held on March 16, none of the 13 candidates in the fray received an absolute majority of votes with Caputova and Sefcovic getting 40.57 per cent and 18.66 per cent respectively.
During vote counting, Caputova emerged as the frontrunner for the presidential post and the official results were declared on Sunday by Slovakia's election commission.
Kuciak was looking into links between Slovak politicians and organised crime and the police believed that he was killed due to his nature of work.