With 99 percent of the vote counted, according to the State Election Commission, Pahor had 47.1 percent of the vote. In next month's runoff, he will face Marjan Sarec, the mayor of the city of Kamnik, who took 25 percent. Turnout reached 43.5 percent.
The result contradicted exit polls by TV Slovenia that showed Pahor winning in the first round.
"In the second round anything is possible, although Pahor is a big favourite," Peter Jancic, the editor of political website Spletni Casopis told Reuters.
Although the office is mostly ceremonial, the president leads the army and also nominates several top officials, including the central bank governor. Most of his nominations have to be confirmed by parliament.
The vote amounted to a warning for Prime Minister Miro Cerar and his Party of Modern Centre (SMC) before the general election due next June or July. Its candidate, Education Minister Maja Makovec Brencic, took only 1.7 percent of the vote and came seventh out of nine candidates.
"SMC will surely have a lot to show at parliamentary election," Cerar told TV Slovenia. "We have a lot of ideas for the future."
Pahor, 53, who ran as an independent candidate, is a former long-time leader of the centre-left Social Democrats. He told reporters he will focus on "connecting people, cooperation, political stability and security" if he wins in the second round.
He was Slovenia's prime minister from 2008 to 2012, the years that led to the worst financial crisis in Slovenia's history. In 2013, the country only narrowly avoided an international bailout for its banks.
A former fashion model, he is also known as the "king of the Instagram", for posting photos on Instagram showing him in his official duties but also in various sports activities.
Sarec, 39, is not affiliated with parliamentary parties but is running as a candidate of his own non-parliamentary, centre-left party, Lista Marjana Sarca. He is a former actor.
"I am happy about this result, which shows that us mayors do a lot for people at the local level and are working hard," he said.
