The face-off, on January 26-27, is shaping up to be a clash not only of politics, but also personalities.
The vote, likely to end in a run-off in two weeks, is seen as a referendum on 73-year-old Zeman, in office since 2013, who has harshly criticized migration from Muslim countries and is keen to boost ties with Russian Federation and China. Zeman is followed by pro-EU candidate Jiri Drahos, a 68-year-old chemistry professor and former chief of the academy of science, with 25.3 percent of the votes.
As a member of an increasingly right-wing regional alliance of Central European nations, named the Visegrad Group, that includes Hungary, Poland and Slovakia, the Czech Republic stands at an ideological crossroads with the rise of the country's xenophobic far right, which rose to parliament in October's legislative elections. CSU will release the results on its website, and the final results are to be available on Saturday evening.
However, in a press conference given with the vote-counting almost over, Zeman said he is ready to conduct live debates with Drahos.
"If Drahos wins, the image of the president will be different than in the Zeman era because Drahos is an intellectual without a radical vision or appeals", said Lubomir Kopecek, a political analyst at Masaryk University in the city of Brno.
He is also stridently anti-Muslim, having once called the 2015 migrant crisis "an organised invasion" of Europe and insisted Muslims were "impossible to integrate". A mild-mannered liberal centrist whom critics have dubbed "wishy-washy", he has called for Prague to "play a more active role in the EU" and has backed the adoption of the euro currency. Zeman was shocked and was took out of the room by two security guards.
"This looks hopeful", Mr Drahos told supporters and reporters at a Prague theatre after most results had come in.
Zeman and Babis are among the most popular politicians in the country of 10.6 million that is largely eurosceptic and rejects accepting migrants from the Middle East and Africa. "It's clear that not everyone can agree, but the current president doesn't unite people, he divides them", Drahos added. Songwriter Michal Horacek finished fourth with 9.2 percent, ahead of physician Marek Hilser, who had 8.8 percent.
"The polarisation of society has deepened in the past months", Saradin said.
Zeman says he is ready "to meet (Drahos') request" to face each other. He has appointed billionaire Andrej Babis, with whom he shares dislike for the EU's refugee policies, as prime minister, even though the tycoon's single-party government doesn't have a majority in parliament.
In turn, Babis has said he'd vote for Zeman, who also spoke at the congress of the Freedom and Direct Democracy, a anti-establishment party that has called for Czechs to harass Muslims and also leave the European Union.
Zeman was quickly escorted out and returned to cast his vote shortly afterwards.
The CTK news agency pegged turnout at 40% after day one of voting. The two candidates with the strongest support will advance to the second round.