Rev Rola Sleiman was invited by the Kirk to attend their annual meeting and said its world mission council confirmed to the UK Visas and Immigration department last month that her expenses would be covered during her eight-day stay.
She later received a letter saying her visa application had been unsuccessful because the UK government was not convinced about claims concerning her incomes or that her expenses during the trip would be covered.
However, the British Embassy in Amman, Jordan has now informed the World Mission Council that it has reviewed her case and has decided to grant her permission to enter the UK.
Reacting to the decision, the Very Rev Dr John Chalmers, Principal Clerk to the General Assembly of the Church of Scotland, said: "We are grateful to the Home Office who have heard our request and granted a visa waiver enabling the Rev Rola Sleiman to travel and join us at the General Assembly in Edinburgh.
"It was clear from the support that we received overnight from the media, the public and the church that people felt a mistake had been made and an important voice might be missing from our Assembly.
"In the end common sense prevailed and it has all happened in time for us to complete Rola's travel arrangements.
"We now look forward to welcoming her."
He had told Premier before the visa was granted that he was hopeful the Home Office would eventually grant the visa.
Rev Sleiman who holds a Syrian passport is now expected to attend the Church's General Assembly on Saturday and represent the National Evangelical (Protestant) Church of Syria and Lebanon at the assembly services at St Giles on Sunday.
