A non-aligned centrist who made his fortune in the consumer-credit business, the 51-year-old Kiska will be Slovakia's first president since independence in 1993 without a past in the Communist party.
"I want to reestablish the people's trust into the presidential office," Kiska yesterday said in a victory speech at his campaign headquarters in the capital Bratislava.
"I want to make the politics more human," said the millionaire-turned-philanthropist who has given away most of his fortune to charity.
"I want to congratulate to Mr Kiska on becoming the new president of the Slovak Republic," he told reporters at his Smer Social Democratic party headquarters in central Bratislava.
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Based on results from 99 per cent of voting districts, Kiska had obtained 59.4 per cent of the vote while Fico had secured 40.6 per cent, the election commission said.
"This election was a referendum on Fico and his government, and he clearly lost it," Grigorij Meseznikov, Bratislava-based analyst from the Institute for Public Affairs told AFP of the premier's failed attempt to tighten his grip on power.
A prospect of Smer winning control of both parliament and the presidency galvanised opponents in the ex-communist country of 5.4 million, which joined the European Union in 2004 and the eurozone in 2009.
Fico's party has a majority 83 seats in the 150-member parliament, with the next general election scheduled for 2016.
Analysts also warned that if he had taken the presidency, Fico could have tried to amend the constitution to boost presidential powers and transform the parliamentary system into a presidential one.