At a meeting on Friday morning five of the seven bishops, 69% of the clergy and 80% of the laity backed proposals to change Canon law governing marriage.
The proposals will now be sent to the church's seven dioceses for consideration and are highly likely to be passed in 12 months.
If passed the Church would become the largest in the UK to offer marriage to same sex couples but it would intensify friction in the wider Anglican Communion.
Primus of the Scottish Episcopal Church Most Revd David Chillingworth told Premier's News Hour the difficulties were "very obvious".
In January the US Episcopal Church was suspended from full participation in the Anglican Communion for the next three years because of its position on gay marriage.
It came about after the Church went against other churches in the Communion by authorising its clergy to perform same sex marriages in July last year.
A meeting was called by the Archbishop of Canterbury Justin Welby designed to stop a break up in the Anglican Communion over the issue.
Bishop David told Premier his main concern is for his own clergy who will not feel able to perform gay marriages.
He said no ministers would be forced to take part and that a Scottish Government law would be used so ministers would have to opt in.
"Our first concern is about the unity and cohesion of our own Church because clearly we have quite a number of people who just couldn't vote for this," he said.
"They believe it's wrong, they believe it's something our Church should not do."
Bishop David speaking to Premier's Aaron James:
