Relative newcomer Zuzana Caputova had 58 per cent of the vote with almost 95 per cent of returns counted in Saturday's runoff election, topping European Commission Vice President Maros Sefcovic, who had 42 per cent.
Sefcovic conceded defeat and congratulated his rival.
"I'm extremely happy about the result," Caputova said. "It's an extremely strong mandate for me," she said.
"Zuzana, Zuzana," her supporters chanted.
Zuzana Caputova reacts as she waits for the results at her election. Source: EPA
Caputova, 45, has little experience in politics and attracted voters who are appalled by corruption and mainstream politics.
She only recently became vice chairman of the Progressive Slovakia, a party so new it has not had a chance to run in parliamentary elections. Caputova resigned from her party post after winning the first round of the presidential vote two weeks ago.
She becomes Slovakia's fifth president since the country gained independence after the split of Czechoslovakia in 1993.
Zuzana Caputova and her daughter Emma. Source: EPA
The president of the nation of 5.4 million people has the power to pick the prime minister, appoint Constitutional Court judges and veto laws. Parliament can override the veto with a simple majority, however. The government, led by the prime minister, possesses most executive powers.
A lawyer, Caputova is a rising star of Slovak politics. She became known for leading a successful fight against a toxic waste dump in her hometown of Pezinok, for which she received the prestigious Goldman Environmental Prize in 2016.
A divorced mother of two, she is in favour of gay rights and opposes a ban on abortion in this conservative Catholic country.
She supported the massive anti-government street protests last year triggered by the slayings of an investigative reporter and his fiancee that that led to the fall of the coalition government. Investigators have linked Jan Kuciak's death to his work probing possible widespread government corruption.
