With almost all results counted, Van der Bellen had 53.3 percent of the vote to Hofer's 46.7 percent.
The election was a re-run of another vote in May, ordered by a court after Mr Van der Bellen won by less than 1%. They and others in Europe had feared that Donald Trump's win in the United States and the Brexit vote in Britain heralded a resurgence of populist sentiment across the continent.
Left-leaning candidate Alexander Van der Bellen says that the presidential election he hopes to win has meaning well beyond Austria.
(Vatican Radio) Austria could get Europe's first far far-right head of state since World War Two following Sunday's presidential election. "And I don't want Austria to leave the European Union".
Data from SORA showed that Van der Bellen's pro-European stance was his supporters' second-strongest reason for voting for him, cited by 65 percent of them, just behind the view that he would best represent Austria overseas. "The European right-wing populists' party is off for now".
Many Austrian Jews, one of Europe's smallest communities with 8,000 members, warned Hofer's popularity might lead the far right in Europe to a significant victory.
He is opposed to an Austrian referendum to leave the European Union, but he advocates popular votes in case Turkey joins the European Union or in case the bloc becomes more centralized.
Now, she said, Austrians will expect Mr. Van der Bellen to mend the rifts that appeared during months of bitter campaigning. While the margin may change when final results are in, Austrian officials said the results gave Van der Bellen an unbeatable lead.
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On Sunday, after casting his ballot, Van der Bellen said the Austrian election was "of significance for all of Europe".
An array of establishment figures lined up behind Mr. Van der Bellen, but Mr. Hofer garnered support from mainstream conservatives in the People's Party, which declined to throw its weight behind the former Greens leader.
The opposition party has been leading in national polls for more than a year, putting them in a strong position to win the 2018 parliamentary elections.
Austrian Presidential candidate Alexander Van der Bellen makes a press statement in Vienna, Dec. 4, 2016.
The far-right candidate in Austria's presidential election has congratulated his independent rival shortly after polls closed.
Following his victory in May, which was later annulled, Van der Bellen told CNN's Christiane Amanpour that Europe "shouldn't dramatize" the growing popularity of far-right parties in Europe.
When Norbert Hofer of the anti-immigration and anti-Islam Freedom Party (FPO) narrowly lost the original run-off in May with 49.65 percent of the vote, European governments breathed a sigh of relief.
His comments reflected his party's modified message. Although this paved the way for a straight runoff between Hofer and Van der Bellen, the Green was considered the favorite. Although the battle for the presidency is over, Austria's larger, ongoing political struggle now enters its next stage.