It's after the country's parliament approved a change in legislation in March, allowing two people of the same gender to marry.
There was enough opposition to the move to trigger a referendum on it, though.
In it, 63% of Slovenians signalled their opposition to the law change with 37% saying their supported the change.
The vote means that the amendment is officially repealed, however politicians from the party United Left have said attempts to bring gay marriage back in would continue.
Pope Francis specifically spoke about the Slovenian referendum before it happened on the weekend, urging voters to "back the family as the structural reference point for the life of society".
The organisation Children Are At Stake, which is backed by the Catholic Church, has been one of the groups spearheading opposition to gay marriage.
Ales Primc, from the group, told the BBC: "This result presents a victory for our children."
However Boris Dittrich, from Human Rights Watch, said: "The rights of a minority, particularly to equality, shouldn't be subject to removal by the whim of the majority.
"No societal problems have emerged in any country after marriage equality that can be attributed to same-sex couples having the right to marry."
