Tycoon Andrej Kiska, standing for office for the first time, defeated current PM Robert Fico in the second round of voting.
Early poll counts suggested Andrej Kiska had gained about 60% of the vote.
Andrej Kiska’s victory stopped Robert Fico’s social democrats from gaining control of both the presidency and parliament.
Correspondents say the prospect of social-democrat domination appeared to galvanized Robert Fico’s opponents.
Robert Fico ended his campaign by wooing voters with tales of his traditional Catholic upbringing in an attempt to appeal to Slovakia’s majority Catholic population.
He portrayed Andrej Kiska as a scientologist, a claim the tycoon denies.
Robert Fico has been in office since the 2012 elections, which saw a party securing an absolute majority in the Slovak parliament for the first time since independence.
“It’s a new feeling to be voting for myself,” said Andrej Kiska, who has never previously run for office, as he cast his ballot in his provincial hometown of Poprad, in northern Slovakia.
France’s President Francois Hollande and European Parliament chief Martin Schulz had both backed fellow leftist Robert Fico.
Andrej Kiska capitalized on his image as a newcomer untainted by allegations of corruption that have ravaged Slovakia’s right-wing.
With no communist past, he is seen as a skilled businessman. He says he wants to fight corruption and create a more efficient government.
Andrej Kiska will be sworn in on June 15, when leftist incumbent Ivan Gasparovic’s second term ends.
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