The saga began with the May election, narrowly won by Mr Van der Bellen, which was overturned due to irregularities in the counting procedure.
Europe is watching the vote with interest and trepidation if Hofer wins he will be the first far-right head of a European state.
After Brexit and Trump and changes in the political landscape in Spain and Greece EU leaders will be hoping for a Van Der Bellen victory.
Fears of a shift to anti-immigration and anti-mainstream parties is gripping Europe with elections in France, Germany and the Netherlands due next year.
Full results are expected Monday evening.