The Rev Ian Watson, of Kirkmuirhill Church near Lanark, South Lanarkshire, was attempting to become the first minister to leave with his flock and their place of worship over the issue of openly gay clergy.
But a vote on whether to quit the Kirk fell short of the two-thirds majority required. The result of the ballot of 282 congregation members was announced at yesterday's service. It showed 104 in favour of staying with the Church, and 114 who wanted to leave. There were two abstentions, two don't-knows and 60 who did not return the form.
But Mr Watson, who earlier said he plans to join the Free Church of Scotland, is due to hold a separate vote in the new year as part of a legal challenge.
The result is a blow to many in the evangelical movement within the Kirk who may have considered leaving because of the appointment of gay minister Rev Scott Rennie to an Aberdeen church in 2009.
A mandate to leave at Kirkmuirhill may also be more difficult to achieve.
It is understood further examination in the test case of the former United Free Presbyterian Church of Scotland building's unusual title deeds - which have a special clause allowing the congregation to change denomination - point to a three-quarters majority rather than two-thirds being required if the congregation decides to switch to another denomination and retain the church.
Bryan Kerr, depute clerk of the Presbytery of Lanark, said: "Following legal advice, it is the opinion of the presbytery that the buildings will remain with the continuing Church of Scotland congregation of Kirkmuirhill Parish Church.
"We realise people for the first time in that community are going to be going to two different churches in a small area and we hope Christian spirit can exist with all those in the debate."
Mr Watson was not available for comment, but a member of the parish said a legal challenge for ownership by the departing congregation was being considered.