"Prolesur and Soprole are both strong businesses but their recent performance has been impacted by challenging market conditions," he said.
"Having the two more closely integrated will generate operating efficiencies across the supply chain from milk collection, to processing and administration," he said.
The remaining 0.1 per cent of Prolesur's shares are held by minority shareholders, which Fonterra will offer to purchase at the same price per share being paid to the Fundación for its shareholding.
Early this year, Chilean charity foundation Isabel Aninat, a 13.6 per cent shareholder in Prolesur, made a complaint against Fonterra's appointed directors on the Prolesur board.
Soprole, a consumer product business operating in the north, sources about 30 per cent of its daily fresh milk from Prolesur. Fonterra, New Zealand's biggest company, said at the time complaint was at an "informal investigation" stage by an appointed prosecutor.