Canon Jeffrey John told the BCC he decided to step down to avoid any damage to the unity of the church.
Archbishop of Canterbury Rowan Williams hailed John's decision to put the good of the church before his own interests and called on congregations worldwide to reflect on what has happened.
Williams also reiterated homosexuals are "full and welcome members of the Church."
The Archbishop also said he was shocked by the number of letters he received opposing John's promotion as well as the "level of ignorance and hatred towards homosexual people."
John was appointed to the bishop's post by Richard Harries, the Bishop of Oxford.
Harries issued a statement saying he accepted John's decision with "great sadness," the BBC said.