Garner was appointed to the position at the end of 2012/2013 season when Ian Holloway was the manager at Selhurst Park.
He had previously coached in the club’s academy.
Garner worked under Holloway, Tony Pulis, Neil Warnock and Alan Pardew at Palace, but he departs ahead of Pardew’s first full season in charge.
Palace chairman Steve Parish told the South London Press: “Alan (Pardew) wanted to do something slightly different.
“We offered Ben a role linking academy players to the first team and he said he wanted to work day-to-day coaching and would rather go than take the new role.
“It is all very amicable. Ben wants to get a manager or assistant manager’s role.
“We wish him nothing but the best. He has a great future in the game and we will miss him.”