“After a terrific 3 ½ years working together, Paul and I have decided to move on to the next chapter in our professional lives,” said Federer, in a statement on his website.
“When we started together we had a vision of a three-year plan to win another Grand Slam title and get back to the number one [Emirates ATP] ranking. Along with many other goals and great memories, these two main goals were achieved.
“After numerous conversations culminating at the end of our most recent training block, we felt like this was the best time and path for both of us.
“Paul remains a dear friend, and we both look forward to continuing our friendship. I want to thank Paul for his help and the value he has added to me and my team.”
The pair joined forced in July 2010 and Federer has won 13 titles, including 2012 Wimbledon.
Severin Luthi, who shared coaching duties with Annacone, is now Federer’s only coach.
The 32-year-old Federer is currently in eighth position in the Emirates ATP Race To London. There are four spots left up for grabs at the elite eight-player Barclays ATP World Tour Finals, to be held at The O2 from 4-11 November.