Parliament approved the introduction of gay marriage through the new Marriage Equality Act with Nationalist MP Edwin Vassallo voting against, while all other MPs voted in favour.
Malta became the 15th EU state to introduce same-sex marriage, just six years after the introduction of divorce.
Clarifying his vote, Mr Vassallo said he could not reconcile his principles with a Bill that was "immoral".
Although he agreed that the state and church should be separate, he said he was a Christian and could not abandon his religious beliefs on parliament's doorstep.
Earlier, the Prime Minister had said that this was a historic moment and invited all MPs to stand up and declare their vote.
In a statement, the government said that the aim of the law was to modernise marriage law through the mainstreaming of equality for all, which means that the institution of marriage is now fully gender neutral to ensure that lesbian, gay, bisexual, trans, intersex, and genderqueer (LGBTIQ) persons are free to contract a marriage with their loved ones, be they of the same or a different sex, and also to parent children without having unnecessary references to their gender or biological make-up on their children’s birth certificates.