The 34-year-old reached the Wimbledon and US Open finals this year but lost both to Novak Djokovic.
In a statement, the Swiss 17-time Grand Slam winner said it was a "dream come true" to work with the Swede, who he described as "my childhood idol".
Severin Luthi will continue to be Federer's main coach but will be joined by Croat Ivan Ljubicic.
Ljubicic, 36, reached a career high of third in the world rankings and won 10 ATP titles.
Edberg, who won six Slams himself as a player in the 1980s and '90s, helped Federer adopt a more attacking approach, frequently utilising serve and volley tactics.
Under Edberg, the Swiss won five ATP titles in 2014 and six more this year.
Federer added: "Although it was only supposed to be for 2014, Stefan was great and agreed to extend the partnership through this year which I really appreciated.
"He taught me so much and his influence on my game will remain. He will always be a part of my team."
Edberg also said the "time commitment" was the reason for the split, adding: "Roger still has a lot left to give to the sport of tennis and is capable of winning the big events."
World number three Roger Federer has split with coach Stefan Edberg after working together for two years.