The deal comes after Synlait said this year it would move into new categories and branded consumer goods, provided it didn't conflict with existing partnerships.
The new facility will have a minimum annual capacity of 110 million litres and be capable of producing pasteurised milk and cream for domestic use, extended shelf life dairy products, long-life milk and cream for export, ready-to-drink liquid infant formula and toddlers milks and other blended dairy-based beverage products, it said.
Analysts have said Synlait would seek to 'de-risk' investment in new facilities by securing a foundation customer.
Discussing the move into new markets on a conference call in September, chief executive John Penno Synlait saw "areas in new categories that could be Synlait branded".
Steve Anderson, CEO of Foodstuffs South Island, said that "in time, we are looking forward to collaborating with Synlait to create a range of new and innovative dairy-based products that our customers will enjoy."
Last month, Penno announced he will step down after 12 years leading the company.
Synlait shares rose 4.6 per cent to $6.99 and have soared 125 per cent this year.