The New Zealand dairy co-operative purchased its share holding in 2013. It sold the stake for A$74m (US$52.6m).
CFO Lukas Paravicini said: "We are focused on investing in higher value-add dairy products that deliver the best returns for our shareholders. Releasing capital such as through this sale, for future growth, is the best use of our shareholders' funds.
Fonterra said the stake sale had no implications for its long-standing relationship with BEGA Cheese, which includes a licence on the Bega brand in Australia and a supply contract for cheese.
"The Bega brand has an important role in our cheese portfolio where we are a market leader and we will continue to build on our relationship with Bega which goes back more than a decade," Paravicini added.