President Milos Zeman and Jiri Drahos advanced to the second round of voting after none of the nine candidates seeking the largely ceremonial post received a majority in the first round two weeks ago.
The election was said to be a referendum on Zeman who is the last prominent figure among active politicians from the country's transitional period in the 1990s.
Immigration was a key issue, more than two years after the European Union first faced a major influx of refugees nearly none of whom ever appeared in the Czech Republic. He has pleased some but alienated others by publicly belittling opponents ranging from the last prime minister to intellectual elites and the press.
Zeman was one of the few European leaders to endorse Donald Trump's bid for the White House.
His stance toward Brussels has been lukewarm.
He flew the European Union flag at Prague Castle, but proposed a referendum on the country's membership in the bloc after Britain made a decision to leave.
Speaking to supporters after claiming victory, Zeman said he would continue travelling the country to meet citizens and hear their worries.
Milos ZemanMilos Zeman was long-time leader of the center-left Social Democrats, before founding the populist Party of Civic Rights in 2009.The tough-talking 73-year-old Zeman, known for his inflammatory remarks against the European Union, immigrants, Islam, the media and urban elites, was Prime Minister from 1998 to 2002 before being elected President in 2013.
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Zeman has benefited from rising hostility to immigration, especially to people coming from Muslim states, although the country of 10.6mn received just 116 asylum applications between January and November past year and has only a tiny Muslim community.
"It is clear that Jiri Drahoš is unequivocally pro-EU and an euro-Atlantic candidate".
Voting in Prague, Zeman slammed political novice Drahos, dubbing him a rival "who hasn't dealt with politics yet", while Drahos vowed the energy generated during the campaign "won't be wasted, whatever the outcome".
The two presidential candidates were as dissimilar personally as they are politically. Zeman is brash, with a self-advertised appetite for alcohol and tobacco. Drahoš is a soft-spoken chemistry professor.
"I am thankful for the enormous wave of energy that has surged with this election", he said, an arm draped around his wife's shoulder. "And I am convinced that it will not disappear".
Zeman also backs Babiš and had pledged to give Babiš a second chance to form a government regardless of the election result. Babis' populist Ano party won the parliamentary election in October.
Zeman's win may strengthen the position of billionaire Premier Andrej Babis, whose minority administration was forced to resign after lawmakers rejected his cabinet in a confidence motion this month.