The meeting was facilitated by the Council of Christians and Jews in response to concerns over a report published by the Church and Society Council for discussion at the Kirk's forthcoming General Assembly.
The report gave rise to concerns and "misunderstanding" within the Jewish community as to the Kirk's position on Israel and Palestine.
The Kirk agreed that the report "requires a new introduction to set the context for the report and give clarity about some of the language used".
During the meeting, the Kirk clarified that there was no change to its "long held position of the rights of Israel to exist".
"The Church condemns all violence and acts of terrorism where they happen around the world," it said.
"The Church condemns all things that create a culture of anti-Semitism."
The Church of Scotland added that its concerns about the injustices faced by the Palestinian people "remain firm" but added that these concerns "should not be misunderstood as questioning the right of the State of Israel to exist".
"Sitting round the table and listening to each other more deeply has created a real opportunity for both communities to better understand each other and that this report now becomes a catalyst for continued and growing conversation," the Church said.
The Jewish community was represented in the meeting by the Scottish Council of Jewish Communities, the Board of Deputies of British Jews, the Movement for Reform Judaism, and Rabbis for Human Rights.