Ex-premier Pahor, 54, who took 47.1 percent in a first round in October, is up against Marjan Sarec, 39, a former comic actor and now a local mayor portraying himself as anti-establishment.
Polls published on Friday by the Dnevnik and Delo dailies put the centre-left Pahor on 52-56 percent against 44-47 percent for Sarec, who took 24.9 percent in the first round.
The role of president is largely ceremonial and turnout could be even lower than the 44 percent seen in the first round, meaning Sarec could potentially score a surprise victory.
"Pahor has been rather defensive in the run-off, underlining his achievements, merits and friends, which has seemed unattractive," analyst Miha Kovac said after a final televised debate on Thursday.
"That could turn against him, in particular if turnout is low," Kovac said on state television.
Pahor stepped down as prime minister in 2011 after his government collapsed in the midst of the global financial crisis that drove eurozone member Slovenia close to needing a bailout.
But the following year he won a surprise victory in presidential elections as an independent backed by the Social Democrats (SD), part of the ruling coalition of Prime Minister Miro Cerar.
His campaign for a second term has seen him hike around the country, chatting to voters and posting photos and videos to his legions of followers on social media.
The former model has 40,000 Instagram fans and even more on Twitter, with international media dubbing him the "Instagram president".
However, his detractors call him "Barbie", and Slovenia's first president Milan Kucan accused Pahor of cheapening the role of head of state and using it for self-promotion.
Polls close in the former Yugoslav republic of two million people bordering Austria, Italy, Croatia and Hungary at 7:00 pm (1700 GMT), with partial results expected later in the evening.
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