The 23-year-old Australian successfully defended his title at the world championships in Barcelona last year but missed out on gold in the blue riband sprint at the 2012 Olympics in London by a fingertip.
"Brant has been such an important part of my journey as a professional swimmer, and in shaping me as person," Magnussen said in a statement on Tuesday.
"Those things combined have made this decision incredibly difficult.
"As I launch into this next competitive block, I have resolved that in order to refocus my program, and to achieve a sense of renewed invigoration, part of that change process involves working with a new coach."
Best, the high performance coach at the New South Wales Institute of Sport, guided Magnussen through his breakthrough season of 2010 and the following year prepared him for his stunning victory at the world championships in Shanghai.
Magnussen led an Australia one-two-three to win 100m gold at the Commonwealth Games in Glasgow earlier this year but his season has also been disrupted by back problems and he finished third in the event at the Pan Pacific Championships.
The time of 47.59 seconds he swam in January remains the best of 2014 but despite a string of sub 48-second times over the last few years, Magnussen has not been able to challenge Brazilian Cesar Cielo's 2009 world record of 46.91.
(Reporting by Nick Mulvenney, editing by Greg Stutchbury)
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