"The President and the Chancellor repeated their common position that fences have no place in Europe," the two men said in a statement after a telephone call on the latest developments in the refugee crisis.
Austria and Slovenia have become key transit points for tens of thousands of refugees and migrants seeking to reach northern Europe ahead of the winter.
Both countries complain they have been left in the lurch by their EU peers and have no option but to take tough action to prevent the situation getting out of hand.
They feel especially aggrieved because after Hungary built a razor-wire fence on its border with Serbia, the flood of migrants switched into Croatia which then adopted controls of its own, isolating Slovenia.
The EU's Schengen passport-free area is cherished as one of its most important achievements and the Commission has repeatedly expressed concern that re-imposing border controls threatens its future.
Both Austria and Slovenia are Schengen members.
Austrian Interior Minister Johanna Mikl-Leitner said the proposed fence was "not about shutting down the border."
"This is about ensuring an orderly, controlled entry into our country. Also, a fence has a gate," she said.
The statement issued by Juncker's office said he and Faymann agreed that measures agreed at an emergency summit Sunday of EU and Balkan states had to be "implemented immediately to avoid a human tragedy."
These included the provision of 50,000 reception places in the Western Balkan states and ensuring much better coordination between countries to avoid the unilateral imposition of border controls.
"President Juncker called on Chancellor Faymann to work closely together with the Commission and UNHCR to ensure that the 50,000 objective is reached as soon as possible, including by means of an Austrian contribution," the statement said.