Centre-left ex-premier Pahor, 54, had been touted to win in October, but a record low 44-per cent turnout triggered a repeat vote, with 1.7 million people called back to the ballot box.
Yesterday, Pahor, who took 47.1 per cent in the first round, garnered 53.1 per cent of the ballot in which turnout was around 40.1 per cent, according to near-complete results.
His rival Marjan Sarec, a 39-year-old former comic actor and now a local mayor portraying himself as anti- establishment, gained 46.9 per cent. He had 24.9 per cent in the first round.
Polls published on Friday by the Dnevnik and Delo dailies put Pahor on 52-56 per cent against 44-47 per cent for Sarec.
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"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," he said on state television.
Dubbed the "Instagram president" by the media, former model Pahor hiked around the country to campaign for re- election, chatting to supporters and posting photos and videos to his 40,000 Instagram fans.
Pahor stepped down as prime minister in 2011 after his government collapsed at the height 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, part of the ruling coalition of Prime Minister Miro Cerar.
Slovenia now boasts one of the EU's most impressive growth rates, with four per cent growth forecast for 2018.