It says it will "take all necessary steps to recover all property and assets, including the church and manse buildings, and all monies belonging to the Church of Scotland congregation of St George's Tron".
The move comes after the 500 worshippers became the first entire congregation in Scotland to leave the Kirk in June over gay ordination, with plans to join a more strict denomination.
Kirk lawyers have already moved to freeze the congregation's bank accounts as each faction claims ownership of the historic property.
Worshippers could now find themselves locked out of the 17th-century church.
The Kirk says a Transitional Ministry will be established to lead a team to "work together with others to re-establish the Church of Scotland congregation of St George's Tron and make effective use of the buildings in support of this aim".
The legal test case will set the scene for what could be one of the largest land and property wrangles in Scotland as evangelical congregations prepare to challenge the Kirk's stance on gay ordination at the next General Assembly.
It is the first such court battle to result after the Kirk's stance in allowing the Rev Scott Rennie, who is openly gay, to take up a post in Aberdeen.
The Kirk's General Assembly voted to accept gay clergy provided they had declared their sexuality and were ordained before 2009.
The Rev William Philip, the minister at the church, which is off Buchanan Street, said when he and his flock quit in June it was because the Kirk is on a "trajectory towards normalising such relationships".
The sums involved in the Tron case are significant. The market value of the church is not known but it recently had a £3 million refurbishment, with members of the congregation raising most of the money for the project.
The congregation – which has been a beacon to worshippers like former motorbike racer-turned-evangelist Alex Bedford who was drawn to the parish to preach – raises much of its £500,000 annual income. Tron should put a percentage – based on its average – towards the £46m pay pot for ministers, but it has halted payments.
The current structure is 200 years old but the church has a Presbyterian history dating back to 1687.
As part of the revamp the church organ, which was never used but which blocked views of the church's two stained glass windows, was removed. Plasma screens were put on either side of the cherry wood, glass and steel pulpit to show films, notices and the words of hymns.
A special committee headed by the Very Reverend David Lunan decided on the legal move. He said: "It gave us little joy to bring this report to [Glasgow] Presbytery; there are no winners in this and all we can do is approximate to that which honours our Lord.
"While I am not filled with joy, I am content, I am at peace, that this is the only outcome that will bring closure, and by the grace of God bring healing."
Mr Philip said the church had done everything it could to seek a constructive way forward, and criticised the "hostile response from the Church of Scotland".
Speaking to The Herald, he added: "The congregation is very disappointed by this action and we have been receiving many messages from people in our home city and beyond who are saddened by this action of Glasgow Presbytery.
"We have tried extremely hard to part company reasonably so we are therefore sad that Glasgow Presbytery has instead taken such a hostile approach."