James Allison has left Ferrari as technical director with immediate effect in what is seen as a joint decision, with Mattia Binotto promoted from head of power units to the new chief technical director.
Allison returned to Ferrari three years ago to head up the Italian manufacturer's major restructuring and the first car built under his design won three races in 2015.
Despite considered gains this year Ferrari has struggled to reach the heights of the previous campaign and Allison's departure comes at a key time with focus shifting towards next season ahead of the 2017 regulations revamp.
Allison says he has personally thanked his Ferrari team while wishing them success for the future.
"During the years I spent at Ferrari, at two different stages and covering different roles, I could get to know and appreciate the value of the team and of the people, women and men, which are part of it,” Allison said. "I want to thank them all for the great professional and human experience we shared. I wish everybody a happy future with lots of success."
Ferrari team principal Maurizio Arrivabene said: "The team would like to thank James for his commitment and sacrifice during the time spent together, and wishes him success and serenity for his future endeavours."
Allison rose to prominence as head of aerodynamics at Ferrari during Michael Schumacher's span of F1 dominance between 2000 and 2004, before switching to Renault as deputy technical director, overseeing Fernando Alonso's two titles in 2005 and 2006.
Ferrari president Sergio Marchionne has recently undergone thorough internal restructuring in a bid to reinvigorate the struggling Italian manufacturer.
With Allison departing from Ferrari a host of F1 teams are expected to target the 48-year-old's services, with McLaren having been keen to sign him in 2013 before he opted to return to Ferrari.