More than 1.7 million people were registered to vote on an issue that has stoked heated debate in the former Yugoslav republic, but turnout -- crucial for either side to succeed -- was low.
By 1500 GMT, three hours before polling closed, only 25% of voters had cast their ballots. Either side needs the support of at least 20% of voters in order to win.
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But opponents immediately launched a campaign to reverse the changes, meaning the legislation never came into force and no same-sex couples were able to tie the knot.
A group called "Children Are At Stake" managed to gather the 40,000 signatures necessary to force a referendum.
Even Pope Francis has waded in, urging Slovenians to defend traditional family values.
He said last week he encouraged "everyone, especially those with public responsibility, to support the family, a structural reference point for the life of society".
Same-sex marriage has already been legalised in 18 countries, including 13 in Europe. Ireland last May became the first to approve gay marriage through a referendum.
"I voted yes. Love is love, regardless of everything," said a 24-year-old woman called Ida in the southwestern port city of Koper.
Vojko, a pensioner, said he was also in favour of the changes, but argued that putting the matter to a referendum was a waste of public money.
"It should be experts or the government deciding about this. They should not leave it to us," he said.
"This is throwing money away. Of course I'm for it, but if it turns out to be a 'no', the world will laugh at us."
The issue has divided the country.
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