The 48-year-old former Netherlands international only signed a new contract in December that should have lasted until the summer of 2026.
Overmars had held his current role since 2012 and has been instrumental in the development of the likes of Donny Van De Beek, Matthijs de Ligt, Frenkie De Jong and Hakim Ziyech, all of whom have been sold for big money.
Overmars said: "I am ashamed. Last week I was confronted with reports about my behaviour. And how this has come across to others. Unfortunately, I didn't realise that I was crossing the line with this, but that was made clear to me in recent days. I suddenly felt enormous pressure. I apologise.
"Certainly for someone in my position, this behaviour is unacceptable. I now see that too. But it is too late. I see no other option but to leave Ajax. This also has a major impact on my private situation. That is why I ask everyone to leave me and my family alone."
Supervisory board chairman Leen Meijaard said: "This is a dramatic situation for everyone who is involved in any way. It is devastating for the women who have had to deal with the behaviour. When we heard news of this, we immediately acted, carefully deliberating and weighing what was the best thing to do, all in consultation with CEO Edwin van der Sar and assisted by an external expert.
"Marc is probably the best football director that Ajax has had. We upgraded and extended his contract for a reason. But, unfortunately, he has really gone over the line, so continuing as director was not an option, as he recognised himself. It is extremely painful for everyone. I want to express the wish that everyone involved is given the peace and privacy to process this."
CEO Edwin Van der Sar added: "I find the situation appalling for everyone and I agree with Leen Meijaard's words. In my role, I also feel responsible to help colleagues. A safe sport and working climate is very important. We will pay even more attention to this in the near future.
"Marc and I have been playing together since the early 1990s, first at Ajax and then with the national team and we have been colleagues in the management of Ajax for almost 10 years now. That has now come to a very abrupt end. We are working on something very wonderful here at Ajax, so this news will also be a blow to everyone who cares about Ajax."
