A joint statement from UK Athletics CEO Niels de Vos and Van Commenee on Tuesday confirmed British media reports that the Dutchman would not seek to renew his contract at the end of the year.
"UKA have today confirmed that head coach Charles van Commenee will leave UKA in December," it read.
"The team set to lead British Athletics through the next Olympic cycle and on to the 2017 London world championships will be announced shortly."
The straight-talking Van Commenee said before the July 27-August 12 London Olympics that he would stand down if the team could not achieve his target of eight medals, including one gold.
Britain, led by distance runner Mo Farah who claimed two golds, heptathlete Jessica Ennis and long jumper Greg Rutherford, won six, though four of them were golds.
Half of the tally was amassed in a stunning one-hour spell during the evening of 'Super Saturday' on August 4.
That was not enough, however, for Van Commenee, who took over the job following the 2008 Beijing Games when Britain performed poorly on the track.
"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," Van Commenee said.
"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 its heart in sustaining this culture." Despite the performances of Farah, Ennis and Rutherford, several athletes failed to perform to expectations.
They included triple jumper Phillips Idowu, who went into the Games under an injury cloud and failed to qualify for the final. Idowu's relationship with Van Commenee suffered a public breakdown in the lead up to his competition.
It was not the first time that Van Commenee had fallen out with athletes after several public attacks over the years.
He accused some British athletes of using an "injury culture as an excuse for poor preparation". In 2004 he branded Olympic heptathlon bronze medallist Kelly Sotherton "a wimp" for failing to go all out for silver while after the 2011 world championships he described the men's 4x400m relay team as "appalling, no real effort, unforgivable".
Some of his selections for the 2012 Olympics also caused controversy but he stood by his policy of choosing athletes he thought capable of winning medals.
De Vos thanked Commenee for changing the culture of the sport in Britain.
"Charles has done an excellent job preparing British athletics for the 2012 Olympic Games," he said in the statement.
"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."