Since 8am, a maximum of 80 migrants per day are being allowed to claim asylum in the country, police said.
In addition, Vienna is limiting the daily number of people transiting Austria to seek asylum in a neighbouring country to 3,200.
Once the quotas have been reached, "the borders will be closed," police spokesman Fritz Grundnig told AFP.
He added that due to bad weather, no migrant had arrived at the Austrian-Slovenian frontier since Thursday afternoon.
Vienna's measures -- announced earlier this week along with tougher controls at 12 checkpoints along its southern borders -- drew an angry reaction from the EU on Thursday.
"Such a policy would be plainly incompatible with Austria's obligations under European and international law," European migration commissioner Dimitris Avramopoulos complained in a letter to Austrian Interior Minister Johanna Mikl-Leitner.
European Commission President Jean-Claude Juncker also criticised the proposal. "As far as Austria is concerned I have to say I don't like this decision, we are questioning whether it is within European law, and we will have a friendly discussion," Juncker told a news conference.
But Austrian Chancellor Werner Faymann said there "will be no lifting of the decision," speaking at a two-day EU summit.
Speaking to French radio during the Brussels summit, French President
Francois Hollande bluntly warned the end of Schengen would mean "the end of Europe, in the sense of free circulation among Europeans."
The deep rifts within the 28-nation bloc have opened as a result of
Europe's biggest migration crisis since World War II.
More than 80,000 people -- many of them children -- have endured the
perilous journey across the Aegean Sea since January, with most fleeing war and violence in Syria, Afghanistan and Iraq.
The daily limit on asylum claims is in line with Austria's announcement last month that it would only take in 37,500 asylum seekers this year -- sharply down from the 90,000 it accepted in 2015, making it one of the bloc's highest recipients on a per-basis capita.
Vienna says that the measures are necessary because a German-backed EU plan for Turkey to stem the flow of migrants setting off from its coast is not yet working, and has urged other countries on the Balkans route into Europe to follow suit.
In response, Slovenia, Croatia and Serbia have also tightened their borders.
In 2015, over one million people reached Europe's shores -- nearly half of them Syrians fleeing a civil war that has claimed more than 260,000 lives.
The vast majority enter the EU through Italy and Greece, where they should register, but poor controls mean most are able to continue their journeys to northern Europe.