While the Austrian president’s role is largely ceremonial, the vote is being closely watched around the world as a yardstick of wider anti-establishment sentiment.
If Hofer wins, he would become the first far-right head of state in Western Europe since the end of World War II.
But if Van der Bellen wins, his election would mark a significant change to Austria’s political landscape, which has been dominated by two centrist parties since the end of the war.
The original presidential vote was held in May, with Van der Bellen, a former Green Party leader, defeating Hofer by little more than 30,000 votes in a tightly fought contest decided by mail-in ballots.
Hofer’s party has risen on a populist groundswell sweeping the continent caused by the European Union’s failure to make progress in the ongoing economic and migrant crises.
In contrast, Van der Bellen — a 72-year-old economist whose parents spent time in a refugee camp before settling in Austria — has championed liberal migration policies.
He is an outspoken supporter of gay marriage, and despite his age, he has young fans who organized dance raves in his support.
On Sunday, after casting his ballot, Van der Bellen said the Austrian election was “of significance for all of Europe.”
“Outside of Austria, the election is perceived as something that does not only concern us Austrians,” he said.
But much has changed since then, and populist movements around the world have been gaining steam.
US President-elect Donald Trump’s surprise win last month may boost Hofer’s campaign.
Britain’s “Brexit” vote to leave the EU in a referendum in June sent shockwaves through Brussels, where fears are growing that more member states might consider pulling out of the post-war bloc.
Early in the campaign, Hofer indicated support for Austria’s own referendum on the country’s membership in the EU, but he has since changed his position, preferring to stay in a reformed decentralized union.
CNN’s Laura Goehler contributed to this report.