The sale was announced by Aboitiz Equity Ventures, owner of Pilmico Foods, in a statement to the Philippine Stock Exchange.
ABF's overseas unit paid P100 million (€1.53m) for the stake in the venture, called Pilmico-Mauri.
The joint-venture was formed in 1995 by Pilmico and Australia's Burns Philp.
ABF gained a 50 per cent share when Burns Philp sold its yeast division to the UK company in 2004.
The wholly owned business will now be integrated under ABF's yeast and baking division, AB Mauri.
The business currently operates a yeast factory in Ilagan producing 130 tons per month, mainly for the local bakery market.
It also makes bread improvers and some other bakery ingredients.
However George Bevege, interim general manager of the new, wholly owned business, said AB Mauri will be looking to grow the business quickly, taking a different direction to how it has currently been run.
"We will be looking to expand in the Philippines and add more bakery ingredients," he told AP-Foodtechnology.com.
Baked goods are popular in the Philippines, where the food market is heavily influenced by the US, and the sector has enjoyed good growth in recent years.
Volume sales of bakery products increased by 5 per cent over 2005, according to Euromonitor.
ABF has also been expanding its global yeast business in recent months, announcing new capacity for yeast extracts in Europe and the US.
Yeast is widely used in the food industry for its contribution to taste in a wide variety of products.
The global yeast market is worth around €1.17 billion, and is growing on the back of increasing demand for natural ingredients in processed foods.
ABF's yeast plant in the Philippines is one of its largest in the Asia-Pacific region.