The political newcomer only decided to run for the presidency after the so-called Panama Papers leak in April, which detailed offshore accounts and implicated several senior Icelandic politicians.
Throughout the campaign, Johannesson rode a wave of anti-establishment sentiment, emphasising his non-partisan, independent vision of the presidency.
The victory was especially sweet for the academic as he celebrated his 48th birthday today.
Businesswoman Halla Tomasdottir, also without party affiliation, came second with 27.9 per cent of the ballots.
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Johannesson will now replace Olafur Ragnar Grimsson, 73, after 20 years as head of state.
David Oddsson, a former conservative prime minister and central bank governor who had been Johannesson's closest rival throughout most of the campaign, garnered just 13 per cent of votes.
But the outrage that fuelled mass street protests in April and led to ousting of premier Sigmundur David Gunnlaugsson appeared to have dissipated somewhat in the final days of the campaign, as euphoria erupted over the Icelandic football squad achieving a historic feat in the Euro 2016 football tournament.