He was not asked to resign by Mars Hill, which at its peak had around 14,000 people attending across its numerous church plants.
The 44-year-old was undergoing a voluntary six-week sabbatical while the church was investigating allegations against him.
Several of his paid staff resigned before or during this period.
Mars Hill made the following statement after its investigation into his conduct as senior pastor: "We concluded that Pastor Mark has, at times, been guilty of arrogance, responding to conflict with a quick temper and harsh speech, and leading the staff and elders in a domineering manner.
"While we believe Mark needs to continue to address these areas in his life and leadership, we do not believe him to be disqualified from pastoral ministry.
"Pastor Mark has never been charged with any immorality, illegality or heresy. Most of the charges involved attitudes and behaviors reflected by a domineering style of leadership.
"We found some of the accusations against Pastor Mark to be altogether unfair or untrue.
"Other charges had been previously addressed by Pastor Mark, privately and publicly. Indeed, he had publicly confessed and apologized for a number of the charges against him, some of which occurred as long as 14 years ago."
Below are parts of Mark Driscoll's resignation letter to Mars Hill:
"By God's grace I have pastored Mars Hill Church for 18 years. Today, also by God's grace, and with the full support of my wife Grace, I resign my position as a pastor and elder of Mars Hill. I do so with profound sadness, but also with complete peace.
"I want to thank you for assuring Grace and me that last Saturday that I had not disqualified myself from ministry.
"You have...shared with me that many of those making charges against me declined to meet with you or participate in the review process at all. Consequently, those conducting the review of charges against me began to interview people who had not even been a party to the charges.
"I readily acknowledge I am an imperfect messenger of the gospel of Jesus Christ. There are many things I have confessed and repented of, privately and publicly, as you are well aware. Specifically, I have confessed to past pride, anger and a domineering spirit.
"I do not want to be the source of anything that might detract from our church's mission to lead people to a personal and growing relationship with Jesus Christ.
"Recent months have proven unhealthy for our family - even physically unsafe at times - and we believe the time has now come for the elders to choose new pastoral leadership for Mars Hill.
"Finally, it would be my hope to convey to the wonderful members of the Mars Hill family how deeply my family and I love them, thank them, and point them to their Senior Pastor Jesus Christ who has always been only good to us."
Paul Petry, a former pastor of Mars Hill Church still doesn't think enough has been done to eradicate the alleged problems at the church.
He said: "I hope there is more, I hope what happened yesterday isn't the end of the matter.
"I believe many people were expecting more, and certainly expecting more of the men who had a sacred duty to love the church, to love the people and to love Mark Driscoll.
"I believe in that they failed miserably."
Dr Krish Kandiah is the President of London School of Theology and has previously criticised comments made by Mark Driscoll.
Speaking on Premier's News Hour about the resignation he said: "There still is a fear for me that he hasn't really owned up to some of the stuff that's gone on.
"He apologises that he isn't perfect, and that's right – none of us are.
"I do think they need to get to the bottom of these allegations and work out where he might have been involved in institutional bullying - it looks like [that] from the outside."
Hear the full interview with Dr Krish Kandiah from Premier's News Hour:
Paul Petry,former pastor of Mars Hill Church: