The PMI, a measure of activity in the manufacturing sector, fell to a worse than expected 49.1 from 56.5 in August.
"The New Sales Orders Index lost 9.4 points in September, reflecting the knock-on effects to the wider manufacturing sector from the prolonged strike activity in the vehicle manufacturing sector," said Abdul Davids, head of research at Kagiso Asset Management.
"Intermittent mining sector disruptions and fears about future industrial action may also be weighing on manufacturers".
Kagiso said the PMI was now lower than the PMI readings of China and the eurozone, two of South Africa's main trading partners.
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