"Of course I hoped and prayed that this particular business would be at another stage before I left, and course it is a personal sadness, a deep personal sadness that that is not the case," Dr Rowan Williams told reporters.
"I can only wish the Synod and the [next] Archbishop all good things and every blessing with resolving this in the shortest possible time."
Draft legislation won the required two thirds majority in the House of Bishops and House of Clergy but fell in the House of Laity by six votes.
Across the three Houses, the legislation won over 72% of the votes. In the House of Laity, 64% voted in favour.
The General Synod has already agreed to the principle of women bishops but the legislative process to determine how this will work in practice has now been set back years as new legislation cannot be brought up for discussion again until a new General Synod is elected in several years.
The draft Measure contained a provision for traditionalist parishes that would have allowed them to request alternative oversight by male clergy.
However, they argued in Synod that the provision did not go far enough in meeting their needs and that more time was needed to reach a more acceptable compromise.
The defeat in General Synod comes in spite of majority support in the Diocesan Synods.
The Bishop of Lincoln, the Right Reverend Christopher Lowson, said it was a "very dark day for the Church".
"This is a very sad day indeed, not just for those of us who support the ministry of women, but for the future of the Church, which might very well be gravely damaged by this," said Bishop Christopher Lowson.
He said today's outcome calls for a "broad review" of how General Synod members are elected.
"The Church has suffered a serious credibility problem while it worked on the legislation, and this is a set-back that could cement the Church's reputation as being outdated and out-of-touch."
The bishop plans to meet women clergy from around the diocese next week to discuss the implications of the vote and "to work with them to re-affirm their ministry in the coming years".
Archbishop of Canterbury-elect, the Right Reverend Justin Welby spoke in favour of the legislation in Synod. He said he would be taking stock overnight and listening to what the Archbishops of Canterbury and York say on the matter.
Archbishop Rowan Williams will be making a statement on the vote to General Synod at the start of business on Wednesday.
The Women And The Church group said the failure to pass the legislation was a "devastating blow for the Church of England and the people of this country".
"This vote is a missed opportunity for a whole generation to see women and men sharing fully in the mission, ministry and leadership of the Church of England," the group said.
WATCH Chair, the Reverend Rachel Weir, said: "This is a tragic day for the Church of England after so many years of debate and after all our attempts at compromise.
"Despite this disappointing setback, WATCH will continue to campaign for the full acceptance of women's gifts of leadership in the Church's life."
The Group for Rescinding the Act of Synod (GRAS) said: "We are deeply disappointed that the General Synod has made a decision so out of step with the will of the Church of England as a whole.
"The Synod's decision to reject the Measure cuts right across what the vast majority of men and women in the Church of England long for and shows that our attempts at compromise have been ignored.
"It undermines the validity of the ministry of every ordained woman and sends out a negative message to all women everywhere."
GRAS said it would now be pressing for a single clause measure "at every level".
Dr Lindsay Newcombe, Vice-Chair of Forward in Faith, a group opposing women bishops, had spoken during the Synod debate urging members not to vote for the legislation.
She welcomed the outcome, saying that a vote in favour "would have been a disaster if it had been passed and a disaster for generations to come".
The Bishop of Pontefract, the Right Reverend Anthony Robinson, and the Bishop of Plymouth, the Right Reverend John Ford said the vote had uncovered a "stubborn unease, particularly among lay people, about the Measure that was presented".
In a statement on behalf of the Anglo-Catholic group, the Society of St Wilfred and St Hilda, they said: "Acutely aware of the profound anguish that will now be felt by so many, we believe that it is wise at this point to refrain from analysis of the past or speculation about what the future might hold.
"These are testing times for the Church of England. We pray that we who, between us, have held different opinions on this great matter will be able to find in each other the wisdom and humility we shall need to build a common future."