The votes were 44 for and three against with two abstentions in the House of Bishops, 148 for and 45 against in the House of Clergy, and 132 for and 74 against in the House of Laity.
The House of Bishops will hold an emergency meeting on Wednesday morning following the decision, a Church spokesman said.
BBC: Women bishops: Church of England general synod votes against - BBC News
The announcement, from the Church's House of Bishops, would allow gay clergy to become bishops if they promise to be celibate.
BBC: CofE drops opposition to gay bishops in civil partnerships
But any change in the law is likely to be strongly opposed by Church of England bishops sitting in the House of Lords.
The Church of England's House of Bishops now says it will allow gay clergy to become bishops if they promise to remain celibate.
It called on the House of Bishops to reconvene the talks started in the summer between representatives of different groups, chaired by Bishop Welby.
The synod's House of Bishops announced on Tuesday that it planned to decide next May on a legislative package to bring before the synod in July.
BBC: Women bishops: Backers look to new general synod election
In July last year, the House of Bishops (HoB) said it would review this decision, made in 2005, to decide whether it could also relate to bishops.
BBC: CofE drops opposition to gay bishops in civil partnerships
Any priest looking to become a bishop must undergo a thorough examination of "personal and family circumstances, " according to a statement released by the House of Bishops of the Church of England.
In July last year, the House of Bishops (HoB) said it would review a decision, made in 2005, to allow the ordaining of openly gay clergy to consider whether they should be allowed to become bishops.
"I now believe that for the mission of God to the people of England it is right for women to take up their place in this House of Bishops sitting before you now, " he told the synod.
Others already elected by the House of Bishops to sit on the CNC - effectively removing themselves from the running - include the Bishop of Carlisle, the Right Reverend James Newcome, and the Bishop of Gloucester, the Right Reverend Michael Perham.
"The Diocese of Salisbury is immensely fortunate to have as its new bishop someone of such breadth and depth in his priestly ministry, and the Church of England will be better for having Nick Holtam in the House of Bishops, " she added.
The Rt Rev Graham James, Bishop of Norwich, said on behalf of the House of Bishops that it would be "unjust" to exclude anyone for consideration for the role of bishop who was "seeking to live fully in conformity with the Church's teaching on sexual ethics or other areas of personal life and discipline".
BBC: CofE drops opposition to gay bishops in civil partnerships
The measure was passed by the synod's houses of bishops and clergy but was rejected by the House of Laity.
The proposed legislation for ordination of women bishops was passed by the synod's houses of bishops and clergy but was rejected by the House of Laity last month.
The two archbishops of the church, the Archbishop of Canterbury and the Archbishop of York, along with 24 other bishops, have seats in Parliament in the House of Lords.
He rejected accusations by supporters of women bishops that a well-organised campaign had skewed representation in the House of Laity, which he insisted reflected opinion in the church as a whole.
The Joint Committee on House of Lord Reform says, however, that the number of bishops in the Lords should be reduced from 26 to 12.
The fact that more than a quarter of the House voted against was accounted for by lay members who supported women bishops, but did not wish to split the Church, he said.
The proposed legislation paving the way for women bishops needed to gain two-thirds majority support in each of the synod's three houses - bishops, clergy and laity - but fell short by six votes in the House of Laity.
BBC: Church of England's decision on women bishops was 'wrong'
The measure to allow women to be bishops passed in the synod's Houses of Bishops and Clergy on 20 November, but failed to gain the required two-thirds majority in the House of Laity.
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