Bowles, a 12-year NFL coaching veteran, was 2-1 as Miami's head coach after Tony Sparano was fired. He replaces Johnny Lynn in Philadelphia. The move was announced Monday.
Bowles previously served as the Dolphins assistant head coach/secondary for three seasons (2008-11).
Bowles has also coached for Dallas, Cleveland and the New York Jets.
Bowles was a defensive back at Temple and played eight seasons in the NFL with Washington and San Francisco.