Turnout in the election for the largely ceremonial position of president exceeded 51 per cent of Slovakia's more than four million registered voters.
The figures showed that Radicova won 44.47 per cent of the vote.
The former labour, social affairs and family minister, conceded defeat and congratulated Gasparovic, but made it clear she would stay in the political arena.
"Almost one million votes - I view the support of so many people as a challenge, as a responsibility, as a new beginning," she said.
In the last few days, the campaign has centered around nationalist issues.
'Yes we can'
Radicova, who borrowed the "Yes, we can" campaign slogan of Barack Obama, the US president, won several southern regions inhabited mostly by Slovakia's Hungarian minority who make up 10 per cent of the population.
But analysts had mainly predicted that Gasparovic, who presented himself throughout his campaign as a guarantee of stability and continuity amid the global economic crisis, would win the election.
Some saw the polls as a test of support for Robert Fico, the country's prime minister, who had endorsed Gasparovic.
The president has little political power in Slovakia, where a parliamentary democracy was established in 1993, following the break up of Czechoslovakia.