The Archbishop of Canterbury has apologised to the gay and lesbian community for the "hurt and pain" caused by the church.
The Most Rev Justin Welby said it was a "constant source of deep sadness" that people were persecuted because of their sexuality as he spoke after a meeting of Anglican leaders.
Mr Welby said facing protesters, particularly those from Africa, was a reminder of the "pain and suffering of many LGBTI people around the world".
"For me it's a constant source of deep sadness, the number of people who are persecuted for their sexuality," he said.
"I don't have the right to speak for everyone. I wanted to take this opportunity...to say how sorry I am for the hurt and pain, in the past and present, the church has caused."
Mr Welby spoke after church leaders agreed to sanction the American branch of the Anglican Communion over its views on marriage and homosexuality.
The meeting of Anglican primates in Canterbury, Kent, reached an agreement on measures against the US Episcopal Church, which a statement said had made a "fundamental departure from the faith and teaching" by endorsing gay marriage.
The agreement upheld a "traditional doctrine" of marriage as being between a man and a woman.
Speaking at a press conference afterwards, Mr Welby admitted the church's decision made it look outdated in some parts of the world such as the UK and the US, but not in others.
He insisted the US Episcopal Church had not been sanctioned but had faced "consequences", and the decision was supported by the "overwhelming majority" of Anglican primates.
The summit aimed to avert a permanent divide in the Anglican Communion amid conflict dating back to the liberal church's consecration of Canon Gene Robinson, who is gay, as bishop of New Hampshire in 2003.
The primates' statement said: "The traditional doctrine of the church in view of the teaching of scripture, upholds marriage as between a man and a woman in faithful, life-long union. The majority of those gathered reaffirm this teaching."
The head of the Episcopalian church said gays and lesbians would experience "great pain" from the decision and "the exclusion or segregation of anybody is not the way of God".
Presiding Bishop Michael Curry said: "All people are God's children and that we're all created equal in God's eyes. Those who are baptised followers of Jesus - whether they are straight gay, lesbian, bisexual or transgendered - if they're committed to following the way of Jesus, they should have equal access to all of the services and sacraments in the life of the church.
Speaking to BBC Radio 4's World Tonight, he compared the experience of the gay and lesbian community to that of the African-American community "who were excluded and segregated".
He added: "This decision is going to bring great pain for people in our church who really believe that this is supposed to be a house of prayer for all people."
The Episcopalian church has been banned from taking part in ecumenical and interfaith bodies, internal committees or votes on doctrine or polity for a period of three years.
The Anglican leaders said there was a "unanimous desire to walk together" and the divisions had caused "deep pain throughout our Communion".
The decision was met with dismay by some including senior Labour MP and former Anglican minister Chris Bryant, who is gay.
He tweeted: "I've finally given up on Anglican church today after its love-empty decision on sexuality. One day it will seem wrong as supporting slavery."