The firm, which floated its former subsidiary on the stock market in 1999 but kept almost one-third of the shares, will use the money to cut debts and improve scope for enlarging its business.
Investment bank Goldman Sachs bought the stake, amounting to 42m shares, and aims to sell it on to financial investors.
Werner Wenning, Bayers management board chairman, said the deal was in line with his goal of enhancing the groups structure made up of 350 companies in crop science and pharmaceuticals.
Bayer shelved the sale of its remaining stake last March because of declining stock markets across the world and a drop in Agfas performance.
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