In reaction, Serbia said it would close its borders with Macedonia and Bulgaria to those without valid documents.
The future of the EU`s passport-free Schengen zone is already in doubt.
Eight of its members, including Austria, Hungary and Slovakia, have tightened border controls, leaving thousands of migrants stranded in Greece.
Europe is facing its biggest refugee crisis since World War Two. Last year, more than a million people entered the EU illegally by boat. Most of them were Syrian, fleeing the country`s civil war.
Slovenia, which is a EU member, has been used as a transit country by migrants trying to reach Germany and other northern European states.
But Slovenian Prime Minister Miro Cerar said on Tuesday the Balkan route was now effectively "shutting down".
He said the restrictions, which came into force at midnight local time (2300 GMT), were part of a wider initiative which would see other Balkan countries, as well as Greece and with the cooperation of Turkey, turn back "all irregular migrants".
The EU and Turkey are considering a radical plan including proposals to return all migrants arriving in Greece sent back to Turkey. For each Syrian sent back, a Syrian in Turkey would be resettled in the EU.
The UN expressed concern at the plan on Tuesday, while Amnesty International called it a death blow to the right to seek asylum.
Speaking to the BBC, Thorbjorn Jagland, Secretary General of the Council of Europe, said the proposal to send migrants back would contravene international law.
The deal, discussed at a summit in Brussels on Monday, has not been finalised and talks will continue ahead of an EU meeting on 17-18 March.
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