The pair's decision to move on from the RFU was widely expected following the resignation of team manager Martin Johnson last month.
Both men came in for criticism in the leaked reports into England's disappointing World Cup campaign and the RFU have since announced that Stuart Lancaster, Graham Rowntree and Andy Farrell will take the reigns for the RBS 6 Nations tournament that begins in February.
"John and Mike have given great service to England and rugby in this country over many years and
their contribution is appreciated," said acting RFU chief executive Stephen Brown.
"As well as his role with the senior team, John has played a major part in developing players as a National Academy coach since he joined the RFU in 2005.
"In his five-and-a-half years with the senior team Mike created one of the best defences in world rugby, and while the World Cup was obviously disappointing overall, it should be noted that England conceded
just three tries in their five matches - the joint lowest in the tournament."
Ford and Wells were both involved at each of the last two World Cups, working first with Brian Ashton and then being kept on by Johnson when he was appointed in 2008.
Their next steps in terms of coaching remain unclear but both were quick to wish England luck without them.
"It has been a real privilege and a great honour to have been involved with the RFU for the last six years. I have been part of a very successful National Academy and England Saxons set up and been to two
World Cups including a World Cup final in 2007, with the victories over Australia in Marseille and France in Paris as stunning highlights with the England team," said Wells.
"I am proud to be leaving at the end of a year in which England has introduced a wealth of young talent, won 10 out of 13 games and are the current Six Nations champions. Now is the right time to move on to look for a new challenge within the game."
"To be England's defence coach over the last five-and-a-half years has been an absolute honour and I have worked with some great players and management," added Ford.
"The World Cup was a watershed and it is time for a new environment. I wish Stuart and everyone the very best for the Six Nations and I firmly believe that England can win it."