Binotto takes over with immediate effect.
Binotto was widely credited with creating cars that were competitive with Mercedes over the past two years - which put a spotlight on questionable strategic choices.
"After four years of untiring commitment and dedication, Maurizio Arrivabene is leaving the team", it read.
"The decision was taken together with the company's top management after lengthy discussions related to Maurizio's long+-term personal interests as well as those of the team itself".
Arrivabene, 61, a former marketing chief with tobacco giant Philip Morris, replaced Marco Mattiacci in 2014, but during his four-year reign Ferrari failed to break Mercedes' stranglehold on the F1 title.
By contrast, Binotto is an engineer with over 20 years of experience with Ferrari, having risen from the role of test engineer to the highest job within the racing team.
The news, first reported by La Gazzetta dello Sport on Monday, comes after Ferrari again lost out to Mercedes in the battle for both drivers' and constructors' championships a year ago, despite beginning the season with perhaps the strongest package on the grid.More news: Clinical Nishikori into Brisbane ATP final
More news: Federer wins record third Hopman
More news: Saudi women get texts to tell them of divorce
A combination of these has meant that Ferrari has won neither the world drivers' nor world constructors' championship since its 2008 triumph when the F2008 won the constructors' title.
Ferrari has won a record 16 constructors' titles and is unique in having competed in every season since the first in 1950.
Arrivabene and Binotto were reported by Autosport to have butted heads over the direction of the Scuderia.
Rival teams had been linked with approaches for the 49-year-old in recent months.
The team meanwhile adopted something of a siege mentality under his leadership. He was promoted to technical chief in July 2016.
Ferrari president John Elkann, who replaced Sergio Marchionne who died past year, has decided Binotto, 49, is the right man to lead the Italian stable in 2019. All technical areas will continue to report directly to Mattia'.
How well equipped he is to fight Ferrari's corner in delicate talks about the sport's future post-2021, with the sport's owners keen to see a more level playing field, remains an open question.
Ferrari enjoyed a strong start to its 2018 campaign, marked by consecutive opening wins in Melbourne and Bahrain for Sebastian Vettel who positioned himself and the Scuderia as the outright favourites for the title, a status the pair sustained over the summer despite the German driver's blunder at his home race at Hockenheim.