This was in the third quarter as strong local demand for imports combined with a weak rand raised the import bill for Africa's biggest economy.
The deficit expanded to 6.8 percent of GDP from a revised 5.9 percent in the second quarter, the South African Reserve Bank said in its December Quarterly Bulletin.
It had previously reported a 6.5 percent gap in the second quarter, but that shortfall dropped after the revenue service started including trade with neighbours Botswana, Lesotho, Namibia and Swaziland, with whom it runs a large surplus.
The Reserve Bank had always produced its own estimates of regional trade flows, but admitted the actual customs figures exceeded its estimates by a "significant margin".
Without the neighbouring countries, the deficit would have been more than 7 percent, bank officials said. The highest deficit in recent history was in Q3 2008 when the gap rose to 7.8 percent of GDP, they added.
The bank said the deficit was financed mainly by direct and portfolio investments, although there are fears these flows may dry up when the U.S. Federal Reserve stops its monetary stimulus programme, making the rand very vulnerable.
The currency has lost about 20 percent against the dollar this year, and retreated briefly after the data to 10.3375 to the dollar before recovering its losses.
Analysts said the yawning deficit and South Africa's relatively small reserves left the rand exposed.
"Given the revision to the past current account deficits, it makes the deterioration in Q3 even more dramatic," said Nomura emerging markets analyst Peter Attard Montalto.
Separately, the Quarterly Bulletin showed spending growth in the economy moderated in the third quarter, with households constrained by tighter lending criteria and slow wage growth.
The finance ministry also put a lid on increased spending by government departments. Growth in spending slowed to an annualised 1.9 percent in the third quarter, from 2.7 percent in the second quarter.