In a statement yesterday, the Chapter of Southwark Cathedral said they were "deeply saddened" to hear that Dr John was not appointed to the role in Wales.
The statement reads: "Southwark Cathedral has a long and proud reputation of standing up for diversity and inclusion within the church.
"It was therefore with deep sadness that we read the reports of the failed appointment process for the vacant see of the Diocese of Llandaff and especially of the way in which it affected the Dean of St Albans, the Very Revd Dr Jeffrey John."
Dr John previously held the position of Canon Chancellor of Southwark Cathedral.
He was in the role when he was forced to withdraw from his appointment to the See of Reading in 2003.
The Cathedral said they "shared in the pain" he and his partner, Fr Grant Holmes, went through when he was denied the appointment.
The Chapter described Dr John as a person of "deep wisdom, the highest integrity and startling honesty".
The statement concluded: "We believe that the church, through its lack of similar integrity, wisdom and honesty, is failing to recognise the God-given abilities from which we as a community benefited.
"We pray for Jeffrey and for Grant, for the Church in Wales and for a future in which discrimination on the grounds of sexuality, gender or ethnicity will cease."
In an open letter last week, Dr John accused the Bishops of Wales of "anti-gay discrimination" after his name was not included in a shortlist of candidates up for the role despite allegedly receiving more than half of the votes in the Electoral College vote.
Church in Wales rules state that because the Electoral College could not come to a decision on a new bishop, the decision is now taken out of their hands and given solely to the five remaining diocese bishops in Wales to make the choice themselves.
A Church in Wales spokesperson told Premier: "
"We understand the disappointment felt by all the candidates considered by the Electoral College who did not secure enough support to be elected as Bishop of Llandaff. However we are satisfied that the Electoral College process was carried out properly and fairly. The meeting was confidential and we will not comment on speculation about the nomination and discussion of candidates. However, we strongly deny allegations of homophobia in the process. Neither homosexuality nor participation in a civil partnership are a bar to any candidate being either nominated or elected as a Bishop in the Church in Wales. Moreover, this was made clear to members of the Electoral College by its President, the Bishop of Swansea and Brecon.
"The Constitution of the Church in Wales requires that an electoral college meets for up to three days and that if the college fails to elect, the decision passes to the Bench of Bishops. The Bishops are now acting carefully in full accordance with the Constitution. Unlike the Electoral College process, there is no fixed timetable for an appointment process, however, the Bishops would wish to announce any appointment made as soon as all necessary formalities are finalised. The appointment process is underway and we see no reason to halt it."
"The Bishops have stressed during the whole process that whoever becomes Bishop of Llandaff, whatever their circumstances, will receive their full support."
Jeffrey John entered into a civil partnership with Grant Holmes in 2006 after a 30 year relationship. They have stated their relationship is celibate.