The FIA confirmed in a statement on Tuesday that Masi, whose job is now shared by Eduardo Freitas and Niels Wittich, had gone.
Masi changed the safety car restart procedure at the end of the Abu Dhabi Grand Prix in December, a move that handed the title to Red Bull's Max Verstappen and denied Mercedes' Lewis Hamilton a record eighth.
He was replaced in February but had remained within the governing body, who had talked about offering him a new role.
A subsequent report into the Abu Dhabi race found in March that Masi had made a "human error" but acted in "good faith".
The FIA said on Tuesday Masi had carried out his various functions "in a professional and dedicated manner" but had decided to return to Australia to be closer to his family and take on new challenges.
He was appointed after the sudden death of Charlie Whiting, who had been race director for decades, in Melbourne on the eve of the 2019 season.
