The Scottish Episcopal Church had made history by voting to allow gay couples to marry in church.
It is the first Anglican Church in the UK to allow gay men and women to marry in church.
The Most Rev David Chillingworth, Primus of the Scottish Episcopal Church, described the vote as a “momentous” step.
The move was made following a ballot at the Church’s General Synod in Edinburgh on Thursday.
The vote approved a motion to remove a doctrinal clause in the canon law on marriage stating it is between a man and a woman.
The result was announced just before 5pm.
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— Scottish Episcopal (@secsynod) June 8, 2017
A “conscience clause” will allow individual churches to opt out of performing same-sex marriages.
The move had to be approved by the church’s three houses: bishops, clergy and laity.
The Most Rev David Chillingworth, Bishop of St Andrews, Dunkeld and Dunblane and Primus of the Scottish Episcopal Church said: “This is the end of a long journey.
“In the life of the church, end points are often also starting points.
“This is a momentous step. By removing gender from our marriage canon, our church now affirms that a same sex couple are not just married but are married in the sight of God.
“They can ‘leave and cleave’. They can express in marriage a commitment to lifelong faithfulness to one another and to the belief that a calling to marriage is for them too a calling to love, forgiveness, sacrifice, truth.
“A new chapter opens up – inclusion has taken a particular form.
“But this same decision is difficult and hurtful for others whose integrity in faith tells them that this decision is unscriptural and profoundly wrong. For them this new chapter will feel like an exclusion – as if their church has moved away from them.
“So the journey which we now begin must also be a journey of reconciliation.”
He added that other churches may reach different conclusions on same-sex marriage.
“Every faith community must face the issues which are bound up with human sexuality – in their own way and in their own time,” he said.
“Others will arrive at answers different from ours.
“I have said this many times before: a vote in General Synod changes the canonical position of our church. But it cannot lay to rest the deep differences which this question exposes in this and every other faith community.”
Same-sex marriage was legalised in Scotland in 2014 but the Episcopal Church is the first to allow gay couples to marry in a British church.
The US Episcopal Church approved gay marriage in church last year.
Last month the Church of Scotland’s General Assembly approved a report which said it should carry out more work on how same-sex marriages could take place in their churches.
