The McLaren boss will be replaced by the head of the Formula 1 programme at Alfa Romeo/Sauber, who will be named as Frederic Vasseur's replacement.
The Frenchman has been Alfa Romeo/Sauber's managing director for a year.
The Italian team will be turned into one that can win the world championship.
McLaren has a team principal.
The car that began the year as the fastest through a series of operational and reliability issues was wasted by Ferrari.
Fred has been able to combine his technical strengths as a trained engineer with a consistent ability to bring out the best in his drivers and teams.
This approach and his leadership are what we need to pushFerrari forward.
Vasseur said he was "delighted and honoured" to take on the leadership of the company.
He said that Ferrari has always represented the very pinnacle of the racing world to him.
I am looking forward to working with the team in Maranello to honor the history and heritage of the Scuderia and deliver for our tifosi around the world.
The appointment of Vasseur is a break from the strategy of choosing team principals.
Since Jean Todt left at the end of 2007, there has been a search for the leaders of their F1 operations.
Marco Mattiacci, who was head of Ferrari North America, became the new sporting director after the departure of Todt.
Maurizio Arrivabene was a senior executive for the team's title sponsor Philip Morris and has been close to the team's operations for two decades.
At the end of the year, Arrivabene was replaced by Binotto, who had been with the team for many years.
He is an engineer who worked his way up the ranks to become the first boss of the engine department.
In Vasseur, Ferrari have found a man with a background in management and success in the junior categories with the ART team.
As Charles Leclerc's title challenge fell apart, his growing frustration with the way the team was operating was transparent.
Vasseur ran Leclerc in GP3 in 2016 and Formula 2 in 2017: he won the title in both seasons.
Leclerc spoke of his admiration for Vasseur as he accepted his trophy for second place in the championship.
He said thatFerrari is very different from other teams. I can only say that my experience with Fred has been great.
He believed in me and we had a good relationship. The decisions shouldn't be influenced by this. He has always been very straightforward and honest.
Vasseur will be responsible for making sure that the race operations of the team are improved so that they don't make the same mistakes as Leclerc.
He probably wouldn't have won in Monaco, at Silverstone and in Hungary in the year 2022.