He is to leave the post by the end of December before taking up a new position as Master of Magdalene College, Cambridge next January.
Dr Williams said it had been an “immense privilege” to serve as Archbishop of Canterbury and that his resignation had “not been an easy decision”.
“During the time remaining there is much to do, and I ask your prayers and support in this period and beyond," he said.
“I am abidingly grateful to all those friends and colleagues who have so generously supported Jane and myself in these years, and all the many diverse parishes and communities in the Church of England and the wider Anglican Communion that have brought vision, hope and excitement to my own ministry.
“I look forward, with that same support and inspiration, to continuing to serve the Church’s mission and witness as best I can in the years ahead.”
Dr Williams' decade as the spiritual leader of the Anglican Communion saw a difficult split between liberals and traditionalists over human sexuality and women bishops.
The Archbishop of York, Dr John Sentamu, said he had received news of his superior's resignation with "great sadness", but added that Dr Williams' leadership had strengthened the Communion in the face of longstanding divisions.
“The last decade has been a challenging time for the Church of England and the Anglican Communion," he said.
"Thankfully, Archbishop Rowan is a remarkable and gifted leader who has strengthened the bonds of affection.
"Despite his courageous, tireless and holy endeavour, he has been much maligned by people who should have known better. For my part he has been God’s apostle for our time."
The Bishop of Durham, the Rt Rev Justin Whelby, said Dr Williams had brought a “wealth of wisdom and spiritual guidance” to what had been a “very demanding job”.
“He has been incredibly supportive to me personally in ministry and in the taking up of the job here in Durham,” he said.
“I would like to thank him for all his help, encouragement, guidance and spiritual leadership that he has brought to the role and I wish him every best wish his new role as Master of Magdalene College Cambridge."
Dr Williams will continue to carry out all the duties and responsibilities of the Archbishop of Canterbury, both for the Church of England and the Anglican Communion, until the end of the year.
The Crown Nominations Commission will consider in due course the selection of a successor.