Anglican Archbishop of Cape Town Thabo Makgoba spoke out on Saturday about his anguish over a debate which rejected proposals to soften the Church's stance on gay clergy and same-sex marriage.
"A word to our lesbian and gay sisters and brothers: I was deeply pained by the outcome of the debate," said Makgoba in a statement.
His comments followed a synod held in Ekurhuleni on Friday which rejected a proposal to allow bishops to license clergy who identified as LGBTI and are in a same sex civil union to minister in parishes.
The meeting also rejected a proposal that bishops "provide for prayers of blessing to be offered for those in same sex civil unions" - although not actually marry them under Church law.
"The motion failed to achieve a simple majority in any House," said Makgoba.
"I was glad I wear glasses or the synod would have seen the tears. I wanted to be anywhere but in the synod hall. I wished I was at home quietly in Magoebaskloof."
Makgoba said that whenever any church members were in pain, "then I am in pain too."
"The pain on both sides of the debate in synod was palpable and no one celebrated or applauded the outcome," said Makgoba.
Nevertheless he reiterated that bishops still believed that when it came to LGBTI members of the Anglican Church, "you are loved by God and all baptised, believing and faithful persons".
"We recognise that many of you are baptised and confirmed members of the Church and are seeking the pastoral care, moral direction of the Church, and God's transforming power for the living of your lives and the ordering of your relationships."
Makgoba urged these members to "stick with us" and contribute to future deliberations on the matter.
Friday's synod covered Anglican Churches in Angola, Lesotho, Mozambique, Namibia, South Africa, Swaziland and the island of St Helena.
Of these countries, only the South African state allows same-sex civil unions.
As part of a debate on the issue of pastoral care for people in same-sex relationships, the motions were put forward to the three separate "houses" of the Synod: the bishops, clergy and laity.
Put forward as a "controversial motion", the proposal needed to obtain a simple majority in each of the houses, as well as a two-thirds majority overall to pass.
"The bishops voted 16 to six against the motion, the laity 41 to 25 against and the clergy 42 to 34 against," Makgoba said.