Mr Van der Bellen, 78, a former leader of the Greens, has won broad popularity for staying calm during times of national crisis.
They have included the collapse of the government in 2019 and the resignation of chancellor Sebastian Kurz a year ago over corruption allegations, which he denies.
The far-right Freedom Party (FPO) was the only one in parliament to field a candidate against Mr Van der Bellen, who won a much tighter race against an FPO opponent in 2016.
Leaders from all other parties in Parliament backed the president.
The Austrian president performs a largely ceremonial role, but has sweeping powers that mean overseeing periods of transition and turbulence.
The president is the commander in chief of the army and can sack the whole government or the chancellor.
"A majority is easily said, but an absolute majority means more votes than all others combined, and one must take that very seriously," Mr Van der Bellen told national broadcaster ORF.
"I was not at all sure that it would happen but it did, and I am very pleased."
The 78-year-old incumbent received 54.6 per cent support at Sunday’s vote, above the 50 per cent mark needed to avoid a run-off.
The far-right group’s candidate, Walter Rosenkranz, came second with 19.1 per cent of the vote, according to preliminary results that don’t include mail-in ballots. Tassilo Wallentin, a conservative lawyer and columnist, and Dominik Wlazny, a physician founder of the Beer Party, each won about 8 per cent of the vote.
"Alexander Van der Bellen really managed to ensure in the first round that he will be the next president. I congratulate him on that," Mr Rosenkranz told ORF.
The president has steered Austria through its most turbulent post-World War II political period. He’s overseen the formation or dissolution of six Austrian governments since his 2016 election.
He twice swore in Sebastian Kurz as chancellor, first as Europe’s youngest leader then a second time after a secret video in Ibiza toppled Kurz’s coalition partner.
Scandals have continued to dog Austrian governments since then and Chancellor, Karl Nehammer is struggling to keep a fragile coalition together as support for his People’s Party falters.
“It would be wise for political parties to look at what’s going on abroad,” Van der Bellen said late Sunday on public broadcaster ORF, mentioning the right-wing takeover of Italy as an example. The picture changes from election to election, and while these movements are difficult to control, they can endanger democracy, he said.