The shortfall was 5.54 billion rand in October - the largest in a year - and analysts polled by Reuters last week had forecast a deficit of two billion rand, although the figures are notoriously volatile.
Compared with the previous month, exports leaped 17.05 percent while imports rose by 6.39 percent, the South African Revenue Service (Sars) said.
Analysts said the sharp rise in exports was positive, but it would be a mistake to read too much into the figure as there was still heavy pressure on South Africa's current account deficit - its broadest measure of trade in goods and services.
"One of the major threats for the currency going forward is the large current account deficit," said Efficient Research economist Nico Kelder. "As soon as we are not the flavour of the month any more for foreign investors, the currency will take a knock."
South Africa's rand depreciated about 10 percent against the dollar in 2005, but this has made only modest inroads into three years of sustained gains which have eroded exports, hurting corporate profits and prompting job cuts.
The unit was little moved in thin trade at 6.34 to the dollar after the data was released.
Nedbank economist Magan Mistry said that rising prices for gold and platinum - metals which South Africa leads the world in producing - were probably the main factor which boosted exports. Lower global oil prices helped keep a lid on imports. South Africa's cumulative deficit for January to the end of November was 24.876 billion rand versus a shortfall of 15.321 billion over the same period last year, the data from Sars showed.
"All in all I think the trade deficit is larger than anticipated, and that indicates to me perhaps that we are on a structurally higher plane as far as the trade balance is concerned," said Standard Bank economist Johan Botha.
"The currency is so strong that nothing seems to move it, but it could have an impact down the line ...at the moment it is not going to move it very much but if sentiment turns around we could see some effects."
South Africa's current account deficit ballooned to a record 72.9 billion rand ($11.5 billion) in the third quarter of 2005 from 55.5 billion rand in the second, according to data from the central bank.