Under the Czech Constitution, the president picks the prime minister after a general election, one of the office's key responsibilities. CSU will release the results on its website, and the final results are to be available on Saturday evening.
As he voted in Prague on Friday, Zeman was targeted by a bare-breasted anti-Kremlin protester who called him "Putin's slut", referring to Russia's president.
The first round of direct presidential election in the Czech Republic started at 14:00 on Friday.
He is also stridently anti-Muslim, having once called the 2015 migrant crisis "an organized invasion" of Europe and insisted Muslims were "impossible to integrate".
They are views worrying many Czechs, who fear that their country may be backsliding from the democratic system they fought so fervently to achieve during the 1989 Velvet Revolution, which ended four decades under communism.
Most recently, he made derogatory comments about the #MeToo movement.
Independent analyst Jiri Pehe said the vote highlights a "polarised" society. "Data also show a deepening rift between cities and the countryside". That has not been Zeman's way.
While Zeman's backing for Babis may prolong political uncertainty as the cabinet is expected to lose a confidence vote next week, Czech financial assets have been largely immune.
Otherwise, the president has little executive power since the country is run by a government chosen and led by the prime minister.
"I think the most important thing is that we manage to unite our society, as was the case with the previous presidents", she added.
A struggle for Czech identity? In recent years, the increasingly right-wing alliance has moved away from progressive European integration and toward the policy of protecting native-born citizens.
"Ever since the beginning of our statehood a thousand years ago, the Czechs have belonged to the European West".
"There is a big disappointment with Mr. Zeman in that position and he is very clearly focusing on Russian Federation and China and trying much more to cooperate with non-democratic countries so that's the first point that is so important for us", said Marketa Adamova, deputy chairman of the liberal-conservative Top 09 party, which did not float a candidate.
Around 8.4 million Czechs were eligible to cast ballots.
The remaining candidates with a chance to advance are not political newcomers: Mirek Topolanek, who served as prime minister from 2006 to 2009, and Pavel Fischer, a former diplomat.
Zeman's inclination towards far-right groups and his warm relations with Russian Federation and China have split public opinion, with a sizeable chunk of the electorate favouring pro-western candidates, including 68-year-old academic Drahos. Critics say his pro-Russian and anti-migrant rhetoric, scorn for media and support of anti-establishment forces including the far-right party Freedom and Direct Democracy, which advocates leaving the European Union, have overturned the role of the presidency, a job that has traditionally been that of a non-partisan voice of the nation.
Drahos, 68, could not be more different.
The populist president and the chemist-turned-politician will now face each other in a two-day runoff election on January 26-27.
With votes from 97.6 per cent of districts counted, Zeman led the race with 39.0 per cent of votes, while Drahos had won 26.4 per cent.