Zuzana Caputova took 58% of the vote.
An environmental activist has been elected as the first female president of Slovakia.
Relative newcomer Zuzana Caputova took 58% of the vote with almost 95% of returns counted in Saturday’s runoff election, topping European Commission vice president Maros Sefcovic, who took 42%.
Mr Sefcovic conceded defeat and congratulated his rival.
“I’m extremely happy about the result,” Ms Caputova said.
“It’s an extremely strong mandate for me.”
Ms Caputova, 45, has little experience in politics and attracted voters who are angered 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.
Ms 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 following the split of Czechoslovakia in 1993.
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. But parliament can override the veto with a simple majority.
The government, led by the prime minister, possesses most executive powers.
A lawyer by profession, Ms 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 Roman Catholic country.
She was also part of a campaign in 2017 that led to the annulment of pardons granted by former authoritarian prime minister Vladimir Meciar.
Mr Sefcovic, 52, is a career diplomat who was supported by the leftist Smer-Social Democracy party led by former populist prime minister Robert Fico, a major force in Slovak politics that was tarnished by corruption scandals. He campaigned on a traditional family values ticket.
Popular incumbent Andrej Kiska, who did not stand for a second term, backed Ms Caputova in the vote.
The two had supported the massive anti-government street protests last year triggered by the killings of an investigative reporter and his fiancee that led to the fall of Fico’s coalition government.
Investigators have linked Jan Kuciak’s death to his work probing possible widespread government corruption.
Fico’s party has already suffered losses in local elections in November — the first votes since the largest demonstrations in the country since the anti-Communist Velvet Revolution of 1989.