Parliament voted to oust conservative Prime Minister Janez Jansa, after smaller parties left his coalition.
He was accused by the anti-corruption watchdog in January of tax irregularities and has been struggling to implement austerity measures to combat the country's financial crisis.
MPs asked opposition leader Alenka Bratusek to form a new government.
She will become the first woman to lead Slovenia since its independence from Yugoslavia in 1991.
Mr Jansa was elected a year ago, but his government has struggled to contain the country's economic problems.
Slovenia joined the European Union in 2004 and the eurozone in 2007, but its banking sector was hit hard by the financial crisis and the eurozone crisis that followed.
It is currently in a deep recession, with unemployment at more than 12% and GDP expected to shrink by a further 2% this year.
There is speculation that Slovenia will be forced to request an international bailout, as it needs to repay 2bn euros (Â£1.7bn; $2.6bn) of debt in the coming months.
Mr Jansa has faced corruption allegations, but also growing public anger and protests over austerity measures.
Ms Bratusek, who has previously worked in the finance ministry, has voiced her opposition to austerity, saying her priority will be "growth and jobs".
She also plans to avoid requesting a Greece-style bailout. "I say it clear, there will be no Greek scenario in Slovenia," she told parliament.
The government of Slovenia, beset by economic turmoil and allegations of corruption, has fallen.