Lion and CUB both slipped back in the rankings based on company revenue.
The purchase is part of the dairy giant's plans to streamline operations in the country.
Fraser Whineray will join as chief operating officer in early 2020.
Fonterra is scaling back how much milk it sources from Australian farmers.
The sale brings Fonterra's debt reduction efforts to over NZ$1 billion.
The struggling dairy co-operative announced a number of asset write downs and one-off accounting adjustments last month.
Fonterra told employees it was scrapping bonuses and freezing pay hikes of about 7,000 employees.
Food giant Mars will acquire a majority stake in German nutrition company foodspring.