"I am confident that this energy will not disappear, that it will remain for the benefit of the republic", Drahos said in a televised statement, adding that he did not intend to leave public life after the elections. "Among the losers" candidates are Pavel Fischer, former Czech ambassador in France, businessman Michal Horacek and doctor Marek Hilser, who together managed to get about 30 % of the vote, a statement highlights.
Polling stations reopened at 0700 GMT Saturday and were set to close at 1300 GMT, with partial results expected to begin rolling in shortly after.
Petr Vasicek, a Prague artist, told AFP that he chose the "educated and intelligent" Drahos over Zeman who is "pro-Russian and pro-Chinese, which I don't like at all".
Zeman's victory is good news for Babis, who was a runaway victor in parliamentary elections in October with pledges to fight political corruption and run the state better.
Zeman was first with 38.6 percent of the vote, followed by Drahos with 26.6 percent.
While Zeman represents poorer and rural voters with lower education, Drahos appeals to wealthier, well-educated urbanites.
Drahos wished him good health and thanked all who came to vote.
Zeman is promoting cooperation with China and Russian Federation, and opposes accepting refugees from Islamic countries. "It's important for us, for jobs; our country is at the heart of Europe - we can't go in just one direction", he said in Prague.
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 previous year and has only a tiny Muslim community.
In the wake of the 2015 migrant crisis in Europe, the anti-Muslim Zeman staunchly opposed European Union quotas created to distribute asylum seekers across the bloc. This is our country.
The face-off to become Czech head of state for the next five years has been seen as one of stark contrasts epitomised by political veteran Zeman and newcomer Drahoš, 68.
A mild-mannered centrist whom critics have branded "wishy-washy", Drahos wants Prague to "play a more active role in the EU" and backs joining the eurozone.
Drahos fought off allegations of paedophilia and having been a communist police agent, suggesting the accusations were a smear campaign by Russian intelligence with links to Zeman. Despite the fall of the Czech government this week, lead by populist Andrej Babis, Zeman - a former left-wing prime minister, this week asked his ally to try again to form a new administration and has vowed to swear him in again before his term expires on March 8.