A landmark vote yesterday saw the General Assembly of the Church of Scotland vote in favour of the ordination of ministers in same-sex civil partnerships.

The motion was passed by 309 votes in favour and 182 against.

The General Assembly opened yesterday with the installation of new Moderator Rev Dr Angus Morrison, who urged the Church to remain united, even in the midst of difficult decisions. "We are all one family," he said.

One of his first tasks was to chair the vote that would be the final say on the proposed legislation, and the culmination of years of deliberation within the Kirk. In 2013, the Assembly concluded that the Church could not condone same-sex marriages or civil partnerships, but commissioners voted in favour of a proposal that would allow individual congregations to 'opt out' of the Church's official policy on homosexuality, and could choose to employ a gay minister should a vacancy arise.

Then in May last year, the Assembly voted overwhelmingly in favour of a proposal that could lead to the ordination of actively gay ministers, with a majority of 369 to 189. Draft legislation was passed to the 46 individual Presbyteries to debate, and the majority voted in favour of the change.

The Church has now officially adopted the position which maintains a traditional view of marriage between a man and woman, but allows congregations to 'opt out'.

Outgoing Moderator, the Very Rev John Chalmers, said after the vote that it was vital that the Church of Scotland maintain its unity, and focus on what holds it together, rather than what divides it. "There's something else that we have to learn as a Church and that is the power of harmony," he told the Assembly.

"Of course we need the freedom across the Church to shape the life and worship of the Church according to local needs and local gifts...but we cannot go on suffering the pain of internal attacks which are designed to undermine the work or the place of others. It's time to play for the team.

"And let me be very clear here – I am not speaking to one side or another of the theological spectrum. I am speaking to both ends and middle. It is time to stop calling each other names, time to shun the idea that we should define ourselves by our differences and instead define ourselves by what we hold in common - our baptism into Christ, our dependence on God's grace, our will to serve the poor and so on."

Co-ordinator of the Principal Clerk's office, Very Rev David Arnott, stressed that congregations would not be forced to acccept a minister in a civil partnership. "The General Assembly of the Church of Scotland decided today to allow individual Kirk Sessions the possibility of allowing a Nominating Committee to consider an application from a minister living in a civil partnership," he said.

"During a vacancy a Kirk Session may, but only if it so wishes, and after due deliberation, agree to a Nominating Committee accepting an application from such a minister. No Kirk Session may be coerced into doing so against its own wishes. This decision was in line with a majority of presbyteries who voted in favour of such a move."

On Thursday, the Assembly will consider extending the new law to include the ordination of clergy in same-sex marriages.