Jost Capito found success with Volkswagen before joining McLaren
Capito was recruited by former McLaren chairman Ron Dennis last year and took over as chief executive officer midway through the 2016 F1 season.
However, he is understood to have stopped working for the team on a day-to-day basis as early as December and Capito has now officially left McLaren
"Regrettably, we have not been able to find common ground on what is and will be needed to make the team successful again," a McLaren spokesperson said.
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But the team did add that Capito had "a strong commitment to bringing success back to McLaren".
"He wanted to build again a winning team and fully focus on making the McLaren F1 car competitive, with the aim of winning world championships in coming years."
McLaren secured their last F1 World Drivers' Championship in 2008 when Lewis Hamilton triumphed but have not won a constructors' title since 1998.
New team boss Zak Brown is desperate to take the 51-year-old F1 team back to the top of the sport and is in the process of overhauling the set-up at the Woking organisation.
He began in November by placing McLaren Group CEO Ron Dennis on gardening leave and removing him from his active role in the company.
Ron Dennis has been eased out at McLaren
The McLaren Honda F1 car is currently not competitive at the front of the grid
Dennis remains a 25% shareholder but the departure of Capito is seen as the latest in a series of moves to dilute the influence of the 69-year-old.
McLaren have yet to announce a replacement for Capito, whose previous job saw him win three drivers' and constructors' World Rally Championship titles with Volkswagen.