A magistrate in Vienna denied them their marriage license, as did the Vienna administrative court.
With this historic decision, the current restrictions on LGBTQ Austrians will be overturned on December 31, 2018 and marriage equality will be in full effect starting January 1, 2019.
Same-sex couples in Austria could previously enter into a civil partnership.
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The case was brought by two women who have a registered partnership but wanted to get married.
Despite the country's soon-coming legalization of marriage equality, it still lags behind in other rights.
The Court examined and repealed the phrase "different sex", opening marriage up to partners of the same-sex. Austrian homosexuals have been able to enter binding unions since 2010 and were able to adopt children and access fertility treatments like heterosexual couples.
Its constitutional court said the current marriage law violated non-discrimination rules. The country's courts have now ruled that definition cannot remain and have ordered that marriage be made available to all couples. In other countries, including Chile and Taiwan, such legislation is being drafted.
In May 2015, Ireland became the first country to legalise gay marriage by popular vote, with some 62% of the electorate voting in favour of legalisation. This year, Germany and Malta joined the group of European countries in which all couples wishing to legally marry are treated equally. Men who have sex with men are also not allowed to donate blood. The corresponding decision made by the constitutional court of Austria, reports Reuters.
The Court felt not allowing same-sex couples the right to marry was discriminatory.