Overmars’ contract with the Dutch champions had been due to run until 2026, but he agreed to leave the club after discussing his position with fellow football great Edwin van der Sar, now CEO of Ajax.
Overmars, 48, joined Ajax as football director in 2012.
"I am ashamed,” he said, revealing he had been confronted about the messages last week.
“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.”
The contents of the messages he sent to female colleagues at the club have not been revealed.
“Certainly for someone in my position, this behaviour is unacceptable,” he added.
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“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."
Overmars married Chantal van Woensel in May 2013 and the couple have two sons.
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 said: "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 ten 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."
Overmars enjoyed a stellar playing career as a winger, joining Arsenal from Ajax in 1997 and scoring 41 goals over three seasons for the Gunners. He then played for Barcelona for four years before shifting his focus to coaching and management. He also scored 17 goals in 86 appearances for the Netherlands. He won the UEFA Champions League with Ajax in 1995 and the Premier League and FA Cup with Arsenal in ’98.