The move comes after Rev Scott Rennie's appointment received backing
The Church of Scotland has avoided a potentially damaging debate about whether gay people should be allowed to become Kirk ministers.
At its General Assembly in Edinburgh, it was decided instead that a special commission should be set up to consider the matter and report in 2011.
There will be a two-year ban on the future ordination of gay ministers.
The decision follows a vote on Saturday not to prevent an openly gay minister taking up a charge in Aberdeen.
The General Assembly said the Reverend Scott Rennie could become the minister at Queen's Cross Church in Aberdeen.
The decision - in a 326-267 vote - raised fear among traditionalists of a possible split in the Kirk.
It also sparked a motion from the Presbytery of Lochcarron and Skye.
It demanded that the Church of Scotland should not accept anyone to be a minister or a deacon who is involved in a sexual relationship outside of marriage with a man or a woman.
The motion called for the passing of an "overture" that would prohibit anybody whose relationships were not faithful and heterosexual from becoming a minister.
The Kirk has now decided to set up a commission to consider the matter and the motion brought by Ivor Macdonald, a minister on Skye, has been removed.
However, Mr Macdonald urged the new commission to take into account the strong feeling in his parish against gay ministers.
He said: "I know that in my own congregation there was a mood of mourning as the people came to terms with what was felt to have been a rubicon crossed by the church.
"And we trust that the deliberations of this special commission will take into view the feelings that are very real in our presbytery and in other presbyteries: views which we had hoped to bring to the assembly this afternoon, will indeed be given a fair hearing."
The Reverend Angus Morrison told elders and fellow ministers that the special commission would best serve the "peace and unity" of the church.
The two-year moratorium on appointing gay ministers, which will not affect Mr Rennie, was part of a "deliverance", or motion, moved by the Reverend Dr John McPake from Mossneuk church in East Kilbride.
Church members were called upon not to discuss the issue with the media during this period.
The measure met with an angry reaction from the Reverend Alec Shuttleworth, who compared it to MPs who like to "blame the media" for the current expenses row.
The Reverend Ian Watson, an opponent of Mr Rennie's appointment, had called for a decision to be reached without delay.
"We're really tired of this debate," he said.
"I really don't know how much longer the church can sustain this debate".