The decision, which is based on a proposal from the church's governing board, means that the Church of Sweden will conduct wedding ceremonies for both heterosexual and homosexual couples.
The proposal was approved by 176 of 249 voting members.
The decision comes just three days after the 30th anniversary of the date when homosexuality stopped being classified as a disease in Sweden.
“The Synod's decision takes a stance in favour of an inclusive view of people. Regardless of whether one is religious or not, this affects the entire social climate and the view of people's equal value,” Åsa Regnér, head of the Swedish Association for Sexuality Education (RFSU) - the country's largest gay rights group, said in a statement.
In June, the church board took the first step towards permitting same-sex marriages by submitting a petition to the Church of Sweden Synod – the church's highest decision-making body.
The board proposed the church continue to perform wedding ceremonies following new legislation which came into force on May 1st and grants same-sex couples in Sweden the same legal marriage status as heterosexuals.
Current church regulations will likely continue to apply in practice, with some alterations, such as replacing “man and wife” with “lawfully wedded spouses” when a homosexual couple is married.
Individual pastors would also still be able to refuse to perform marriage ceremonies for same-sex couples.
Since 2007, the Church of Sweden, which counts around 74 percent of Swedes as members, has offered gays a religious blessing of their union.
The ruling by the Synod, which has 251 delegates - two of which were absent from Thursday's vote, puts Sweden among the first countries in the world to allow gays to marry in a major church.
Representatives from the Catholic and Orthodox churches in Sweden, however, were disappointed by Thursday's decision.
“It is with great sorry that we receive news that the Church of Sweden's Synod has today decided to wed same-sex couples that it will be referred to as marriage. This is a step backwards, not only from Christian tradition, but also from all of the major world's religions views of what marriage is,” write Vicar Fredrik Emanuelson of the Catholic Church and Father Misha Jaksic, coordinator of the family of Orthodox Churches at the Christian Council of Sweden (CCS), in a joint statement.
“We don't wed same-sex couples in our churches and faith communities because doing so stands in clear opposition to the church's tradition and to our entire view of creation.”
In moving ahead with the decision to perform same-sex marriages, the Church of Sweden also ignored concerns expressed earlier this year by the Church of England in a strongly worded letter to Swedish archbishop Anders Wejryd that the move could lead to “an impairment of the relationships between the churches”.
Church of England spokesperson Steve Jenkins confirmed that relations between the two churches may be headed for a turbulent phase in the wake of the decision.
“Those concerns remain,” he told The Local, referring to the letter from English bishops Christopher Hill and John Hind.
He added that he didn't know of any plans by the English Church to issue a formal statement in response to the Church of Sweden's decision.