The presidents broached a variety of issues, including the status of the Slovenian minority in Austria and the position of the German-speaking community in Slovenia, which wants to be recognised as a minority.
Van der Bellen said the two countries were partners and friends whose relations were underpinned by "human, economic and political ties".
He said the situation of the Slovenian minority there had changed for the better, while there were also positive signals regarding Slovenia's support for the preservation of the German-speaking community in Slovenia.
Pahor stressed that the communities had different constitutional statuses, but he is in favour of Slovenia doing everything it can so that the community can preserve its identity. "This makes us richer," he stressed.
Both presidents expressed support for the idea of a Slovenian-Austrian event marking the 100th anniversary of the referendum under which voters in a large part of Carinthia opted for Austria instead of the Kingdom of Serbs, Croats and Slovenians.
Pahor said the anniversary was an opportunity for a manifestation that would unite both nations and countries. "It is a great opportunity to set things that appeared a historical problem into the context of the future, where they can become solutions."
The pair also discussed Austrian police checks on the border with Slovenia, which Pahor said were unjustified, and construction of a new unit at the Krško nuclear power station, which Pahor indicated would likely be subject to a referendum in Slovenia.
Ven der Bellen said nuclear energy, which Austria has given up long ago, was one of the open issues, a reference to Austria's long-standing opposition to nuclear energy, both existing and new projects, in its neighbourhood.
Pahor said that his official visit was a part of Slovenia's efforts to have excellent relations with all neighbouring countries, noting that Slovenia was trying to resolve problems in dialogue. He expressed pleasure at Slovenia and Austria declaring 2020 as the year of neighbourly dialogue.
Broaching EU topics, in particular EU enlargement to the Balkans, Van der Bellen said that progress with regard to the accession of North Macedonia and Albania was needed in order for the EU to remain credible.
Pahor said the EU's absorption capacity was not questionable since these countries have small populations. He believes the EU Commission must treat Western Balkans as a whole.
The Slovenian president also held talks with Brigitte Bierlein, the new Austrian chancellor, with the pair describing bilateral relations as excellent and expressing the wish for deeper ties in science and culture, according to Pahor's office.
Pahor and Bierlein also expressed the hope that cooperation in 2020, which they declared as the year of neighbourly dialogue, would "nurture and affirm the already good neighbourly relations", with Pahor expressing the conviction that all issues, no matter how complex, can be resolved in dialogue.
The meeting with Speaker Wolfgang Sobotka revolved around international issues, the future of the EU and multilateralism.