Ferrari stalwart Binotto has been technical chief since 2016, when he stepped up to the role following the team's split with James Allison.
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"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".
The Prancing Horse have opted to make the change after a tough 2018 campaign, which saw them fail to win either title despite a promising start to the campaign, with Mercedes securing a fifth successive double world championship.
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It is unclear who will replace Binotto as head of Ferrari's technical department, but there are suggestions the team may elect to hand more responsibility to aero chief Enrico Cardile and the head of its engine department Corrado Iotti.
Ferrari president John Elkann, who replaced Sergio Marchionne who died previous year, has decided Binotto, 49, is the right man to lead the Italian stable in 2019.
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Binotto, who has risen through the ranks to technical director and overseen a big step up in engine performance, had reportedly been a target for rival constructors and Ferrari were determined to retain his services.
Recently, he has been linked with a senior role with Italian football powerhouse Juventus - where he has been an independent board member since 2012.
Binotto was the man it is widely believed former Ferrari President Sergio Marchionne - who passed away last July - had wanted to take the running of the team for next season. In contrast, Binotto has played a huge role in Ferrari's engine gains in recent years as well as their recent improvements on the aero side. In its now decade-long title drought, the Scuderia has become desperate to return to winning form and has burned through team principals faster than any other team on the grid in the V-6 era.