"The merger has been rejected," Marteen van Hoven, manager for mergers and acquisitions at the Competition Commission said on Wednesday.
"The market is highly concentrated at the moment with only three players and the merger would have reduced that to two."
Pioneer Hi-Bred said in brief statement it was disappointed
by the decision and planned to appeal it. DuPont is the world's third largest chemical firm.
South Africa has scuppered cross-border deals in the past. Last year it blocked a $24bn tie-up between local telecom MTN Group [JSE:MTN] and India's Bharti Airtel due to concern that MTN would lose its local listing.
Walmart Stores last month scaled back its bid to buy out retailer Massmart Holdings [JSE:MSM], settling for a controlling stake. Massmart executives said the government had expressed interest in keeping the firm listed locally.Pioneer bid for a controlling stake in Pannar, which operates seed businesses in nine countries in Africa, is the latest move in a race by major agricultural companies to stake a claim in Africa as concerns mount about global food security and population growth.