Leak will coach receivers for the 2014 season.
Phillips said in a statement that he stepped down for ''personal reasons.''
''I'm thankful for the opportunity that the University of Florida and Will Muschamp provided to me and my family, but at this time I have decided to step down from my position on the UF coaching staff for personal reasons,'' Phillips said.
Phillips joined the Florida staff in December 2012 and spent one year coaching Florida's receivers. Prior to that, he was Kentucky's head coach for three seasons (2010-12).
''I appreciate Joker's contributions to our program and wish him and his wife, Leslie, nothing but the best in the future,'' Muschamp said.
Leak, who captained Florida's national championship team in 2006, ended his career as the school's all-time leader in passing yards (11,213), completions (895) and attempts (1,458). He joined Muschamp's staff last May and served as a graduate assistant last season.
''I appreciate the opportunity that Coach Muschamp has given me and my family,'' Leak said. ''It's an honor to be coaching at my alma mater, where I have so many fond memories both on and off the field. We have a tremendous coaching staff, a great group of players and a support system in place, and I'm excited to be a part of it.''
Phillips is the third offensive assistant to leave after last season's 4-8 finish, the program's first losing season since 1979. Offensive coordinator Brent Pease and offensive line coach Tim Davis were fired, replaced by former Duke offensive coordinator Kurt Roper and former USC offensive line coach Mike Summers.
Phillips also is the second receivers coach to resign during Muschamp's four-year tenure, joining Aubrey Hill. Hill left days before the 2012 season, prompting Muschamp to promote graduate assistant Bush Hamdan to receivers coach.
''Chris is a bright young coach,'' Muschamp said. ''He is one of the all-time Gator greats and being at Florida is very important to him. He has been working with Coach Roper and our offensive staff and is very familiar with our players and new system.''