Immigration is a key election issue in one of the EU's most eurosceptic member states.
The vote showed Czech voters' concerns over security despite a period of fast economic growth and rising wages.
Despite the fall of the Czech government this week, led by populist Andrej Babis, Zeman - a former left-wing prime minister - asked his ally to try again to form a new administration. "I will not leave public life", he said.
He also struck an overtly populist tone by insisting that the "intelligence of journalists.(and) some politicians is significantly lower than that of normal citizens".
"We did not win, but we didn't lose either".
His sharp criticism of immigration from Muslim countries has won him favour with large numbers of Czech voters, despite only 116 asylum applications being made between January and November past year.
During the debate, Drahos called Zeman "a representative of the past political era.a symbol of division".
Billboards across the Czech Republic sought to appeal to voters with anti-migrant messages: "Stop immigrants and Drahos".
According to Pehe, his position cast Zeman as "the defender of Czech national interests in the eyes of his supporters".
His rival must overcome voters' suspicions that he is soft on immigration, with public opinion strongly against European Union attempts to impose compulsory quotas for each member state to accept refugees.
Drahos underscored his concerns about possible Russian meddling in the campaign, saying that "for (Russian President) Vladimir Putin's regime, North Atlantic Treaty Organisation is the biggest enemy and we are part of North Atlantic Treaty Organisation".
Another Prague voter Lubos Horcic told AFP he was backing Drahos because "he will work to reconcile society and not divide it like Comrade Zeman", adding that Drahos was "moving towards Europe and the West and not towards the East".
Voter Daniel Hajek said he had chosen Zeman "because he's opening the door to economic cooperation with countries like Russian Federation and China".
"It's important for us, for jobs; our country is at the heart of Europe - we can't go in just one direction", he told AFP in Prague.
Czech TV pegged turnout for round two at 66.6 percent, the highest figure since parliamentary elections in 1998.
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.
But police charges that Babis illegally obtained subsidies as a businessman a decade ago - which he denies - have left his party without ruling partners.
While most executive powers lie with the government, the president names the prime minister, appoints central bankers and commands the military.