This figure includes trade data between South Africa and Botswana, Lesotho, Namibia, and Swaziland (BLNS countries)," spokesperson Adrian Lackay said in a statement.
Exports in September rose by 18.2 to R90.79bn and imports by 0.2% to R93.71bn.
The September data brings the cumulative deficit for the year to R73.74bn, compared with a R63.07bn gap over the same period in 2013.
Precious metals and stones exports increased by R4.84bn, mineral products R3.91bn, vehicles and transport equipment R2.07bn and chemical products R1.04bn.
Base metal exports increased by R883m, machinery and electronics R875m, while other unclassified exports increased by R606m.
Vegetable product exports dropped by R695.
Meanwhile, vegetable product imports increased by R1.3bn, chemical products R631m, base metals R548m, and mineral products increased by R542m.
The import of equipment components dropped by R901m, vehicles and transport equipment R1.13bn, and machinery and electronics by R1.48bn.
South Africa recorded a R16.62bn trade surplus with Africa, having exported goods worth a total of R28.2bn and imported goods worth R11.57bn.
This was a 48.4% increase in comparison to the R11.20bn surplus recorded in August.
READ: Trade deficit soars in August
Trade with the Americas registered an R805m deficit, while trade with Asia showed an R18.13bn deficit.
Trade with Europe saw a R5.12bn deficit, while trade with Oceania registered a R169m deficit.
If trade to Botswana, Lesotho, Namibia, and Swaziland was excluded from South Africa's trade data, the country would have registered a trade deficit of R12.64bn.