The announcement brings to an end what has been widely regarded as a hugely successful Olympic and Paralympic era for Great Britain.
UK Athletics chief Niels de Vos said: “Charles has done an excellent job preparing British Athletics for the 2012 Olympic Games. We have spoken daily for the last four years and have discussed the post 2012 position almost as often.
“He and I have always been aware of the possibility of him leaving and we are confident that our long term plan will enable us to continue building on the success we achieved in London. There is no doubt Charles has helped to transform our culture, and we can now look forward to further success under the leadership of a new team.”
Although Van Commenee's contract is thought to expire at the end of December, he had been quoted as saying before the Games that he would stand down if the team could not achieve his target of eight medals, including at least one gold.
Van Commenee said: “Niels and I have worked hard to implement accountability as it is vital to the culture of elite sport, and this has been absolutely central to what we have achieved here in a short space of time. Whilst I am thankful for the kind comments and wishes I have received in recent weeks, I believe my decision has the interests of British athletics at it’s heart in sustaining this culture.
“I am happy the future is looking promising with the talent that is about to break through now. But now it needs the new energy and approach by the new leadership team through to 2017.
“As CEO Niels has always had an eye on the eventuality of my leaving – indeed he and I have worked together to put in place an excellent succession plan for the sport. I look forward to seeing the future successes for the GB & NI team through to Rio and the World Championships in London.”
Great Britain won six track and field medals at the July 27-Aug. 12 Games, including four golds.
Led by distance runner Mo Farah, who claimed two golds, heptathlete Jessica Ennis and long jumper Greg Rutherford, half of Team GB's tally was amassed in a stunning one-hour spell during the evening of 'Super Saturday' on August 4.
Despite those performances, several athletes failed to perform to expectations, including triple jump hope Phillips Idowu, who went into the Games under an injury cloud and failed to qualify for final.
Idowu's relationship with Van Commenee suffered a public breakdown in the lead up to his competition.
Van Commenee said before the Games: “If I hold athletes and coaches accountable every day, how could I work over the next four years if I am not held accountable myself? It’s a no-brainer. I never understand when people who have failed stay in jobs, as in politics and football.”