The rule change from the two-year-old Northern Church - a union of Protestant churches - was voted in almost unanimously by a summit in Lübeck on Friday by 156 votes to two.
It states that as long as a prospective pastor and his or her same-sex partner are in a "recognized life partnership" (the equivalent of a UK civil partnership), the pair are to be treated the same as heterosexual couples when being considered for entering a parish residence.
The right to live in the clergy's residence is a "symbol" according to Pastor Mathias Benckert, a spokesman for the Northern Church.
Benckert told The Local: "The principles of trust, care, reliability and commitment, all the things that would need to be part of a pastor's marriage – these things also go for a registered life partnership," he said.
The rules guaranteed that clergy, whether gay or straight, would only be chosen if the parish council and the regional supervisor, whose job it is to nominate them, agreed.
The model allows conservative and liberal elements of the church to form a consensus, Benckert said, as if the congregation is not happy with a prospective clergyman or woman, they will not be selected.
"If the provost [supervisor] knows a parish is very conservative, they simply won't suggest a gay candidate," he said.
Benckert added the union had made the advance "a little late" due to the fusion of the previous church authorities of Hamburg, Schleswig-Holstein and Mecklenburg-West Pomerania into the Northern Church in 2012.
Regional church authorities in Braunschweig and Hanover have already enacted rules to accept clergymen and women in committed same-sex relationships.
And despite Protestant clergy voting to rule out any public celebrations of gay unions back in 2000, such celebrations are now quite widespread in churches in Frankfurt and Schleswig-Holstein, Benckert said.
A church in Kurhessen-Waldeck in central Germany even changed the rules in 2013 to allow homosexual unions to be written in church records with the same status as marriages according to the TAZ newspaper.
The Northern Church votes next year on whether to officially welcome the celebration of gay unions in its churches.