The Church of Scotland approved a report on Thursday criticising Israel's policies towards Palestinians.
The General Assembly debated a revised version of "The Inheritance of Abraham" after the original report provoked a strong negative reaction within the Jewish community in the UK and abroad.
The revised report is still critical of Israel but modifications were made to clarify the Kirk's support of Israel's right to exist and its opposition to all forms of anti-Semitism and Islamophobia.
Presenting the report, the Reverend Sally Foster-Fulton, Convener of the Church and Society Council said: "This is primarily a report highlighting the continued occupation by the state of Israel and the injustices faced by the Palestinian people as a consequence. It is not a report criticising the Jewish people.
"Opposing the unjust policies of the state of Israel cannot be equated to anti-Semitism."
The revised report was overwhelmingly accepted by the General Assembly.
Mrs Foster-Fulton said: "The ongoing conflict in Israel and the Occupied Palestinian Territory has been an issue close to the heart of the Church of Scotland – we have a long relationship with the region and have many friends there.
"The Church has kept on thinking about ways we can contribute to a just and peaceful solution."
She acknowledged that the report had caused "no small amount of controversy" but added that the council had learned "a great deal" from dialogue with the Jewish community.
Revisions were made to the original report following a meeting with the Council of Christians and Jews, the Scottish Council of Jewish Communities, the Board of Deputies of British Jews, the Movement for Reform Judaism, and Rabbis for Human Rights.
"We would like to thank members of the Jewish community who sat down with us and were gracious in their concern," Mrs Foster-Fulton said.
The General Assembly heard that the revised report included a new preface that "sets the report more in context".
She said: "While acknowledging that some of the original language, on reflection, was misguided, I want to affirm that the report remains robust. It offers new insights - ones that have come through the experience of those suffering the continuing injustices of occupation."
She added that she was looking forward to continued discussions with the Jewish community "exploring the issues and ideas brought forward in the report".