Australia recorded a 5-0 whitewash of the tourists less than four months on from England's 3-0 summer series victory.
Flower had made it clear, after the final Test defeat in Sydney this month, he intended to continue and try to reinvigorate England alongside captain Alastair Cook.
However new ECB managing director Paul Downton, who officially starts in his post on Saturday, met with Flower at Lord's on Thursday and informed the Zimbabwean his four-and-a-half year tenure had come to an end.
Flower is the third figure within the England set-up who has eventually left his role following a frosty relationship with Kevin Pietersen.
It was reported recently Flower had issued an ultimatum over Pietersen's place in the side, but now he has lost his job England's most naturally gifted batsman can continue his international career.
Although he resigned the captaincy in 2008, Pietersen's uneasy alliance with former coach Peter Moores led to the latter's sacking and Pietersen went on to say: "The team wasn't happy, things weren't right, and England cricket was going nowhere."
And 18 months ago Pietersen was at the centre of more controversy when he sent text messages to South African cricketers - during England's Test series with the Proteas - in which he made disparaging comments about captain Andrew Strauss.
Pietersen was demoted for the final Lord's Test, which proved to be Strauss' last as he retired from cricket soon after. Pietersen was "reintegrated" into the England set-up for the triumphant winter tour of India in 2012.Suggest a correction