The controversial Bill was defeated by just three votes at a meeting of the 140-member body in Lampeter.
Prior to the vote, the Archbishop of Wales, Dr Barry Morgan, had urged the body to accept the Bill, saying he did not see how the Church could "logically exclude women from the episcopate" after the 1996 decision to allow women priests.
He expressed his disappointment after the vote. "I feel we won the argument but we narrowly lost the vote," he said.
"It was lost by just three votes which is very narrow and a great disappointment."
He said that supporters of women bishops "were reluctant to sanction them because they feared it might institutionalise schism".
Whilst the House of Laity and House of Bishops secured the required minimum two-thirds majority in favour, the House of Clerics passed the Bill by only 27 votes to 18, meaning that it missed the required minimum by three votes.
Dr Morgan added, however, that the Bill's defeat did not signal the end of the debate on women bishops within the Church in Wales.
"I think it is three years before this can be brought forward again and the issue will certainly not be going away."
Anglican Churches in Scotland, Ireland, Canada, the US and New Zealand all permit women bishops.
