Members of St George's Tron, in Nelson Mandela Place, who have been locked in a six-month battle with the Kirk, will hold their last service on Sunday.
The congregation was threatened with eviction from the premises after it split from the main church in opposition to the ordination of gay ministers.
Now the church's minister has agreed to leave the building rather than face a lengthy legal battle with the Kirk
Sheriff officers entered the church building on Wednesday evening during a prayer meeting to issue Court of Session interim interdicts on behalf of the Kirk.
Rev Dr Willie Philip, the church minister, accused the Kirk of frightening and humiliating tactics.
He said: "To disrupt a prayer meeting in that way truly beggars belief.
"It is shameful."
The Kirk said it was moving to protect charitable assets and had a duty to provide a ministry at the Tron and maintain stewardship of the buildings.
The Tron's 500-strong congregation plan to move to rented rooms at the Bath Street Halls religious training centre.