The plan will not take effect until 2015, The Scotsman reported. The church, which has a Presbyterian form of government, will spend the next year developing the legal form for allowing gay clergy, followed by votes by the presbyteries and then by another, presumably automatic, vote by the Assembly.
Following 6 hours of heated debate, the Assembly voted to retain its "current doctrine and practice in relation to human sexuality," banning gay clergy, with an opt-out for individual congregations.
"This is a massive vote for the peace and unity of the Church," the Right Rev. Lorna Hood, moderator of the General Assembly, said.
The issue has split the church, often called the Kirk, since 2009 when the Assembly allowed Queen's Cross Church in Aberdeen to call the Rev. Scott Rennie as its minister. Rennie, who had been married and divorced, was in a committed same-sex relationship.
At the same time, the Assembly placed a moratorium on further approval of gay clergy. At least one congregation in Glasgow has left the church because its members perceived it as moving towards gay clergy.
Evangelicals warned of further departures, saying they had been betrayed by the compromise.