The central bank also said violent unrest in the mining sector, in particular fallout from the police shooting of 34 striking miners at a platinum mine last month, might cause economic growth to slump in the third quarter.
In its latest Quarterly Bulletin, reporting on the second quarter, the bank said the current account gap widened to R200-billion or 6.4% of GDP from 4.9 percent in the first quarter, while spending on government wages pushed gross domestic expenditure to 4.7%.
"With South Africa's terms of trade also registering a modest further deterioration, the deficit on the current account widened to 6.4% of GDP," the central bank report said.
Economists had expected a deficit of only 4.7% because of increased portfolio inflows into emerging markets, and South Africa specifically.
Africa's biggest economy is due to join the prestigious Citi World Government Bond Index (WGBI) on October 1 and foreigners have flooded into the local bond market in anticipation of the inclusion, which will force index-tracking investors to increase their holdings of local debt.
Local investment houses have reported increased business since the Citigroup announcement in April, while bond yields have continually tested record lows.
The increased bond inflows resulted in a financial account surplus in the quarter, the bank said, although analysts said this could not last forever, suggesting the rand was vulnerable if global appetite for emerging market assets switched.
"This is an unsustainable current account deficit," said Kevin Lings, chief economist at Stanlib.
"What is bailing us out is our inclusion in the Global Bond Index, which has resulted in the massive inflows into our bond market. We will still end up with a record inflow into the bond market and that is what is helping us to finance this."
The rand eased after the data, hitting 8.2225 at 0915 GMT from 8.21 moments before the release.
Although economists agree that the deficit will be comfortably funded by foreign portfolio inflows, a further deterioration in the current account could make it unsustainable.
The central bank surprised the market by reducing rates for the first time in 20 months in July, putting the repo rate at which it lends to commercial banks at a 40-year low of 5%.
However, a jump in household and government spending in the second quarter caused some economists to wonder whether this decision would be reversed shortly.
"When you look at the driver of it, it is very clearly household and government debt which is expanding at a time when South Africa's production is under massive pressure," said George Glynos, managing director at ETM.
"It raises questions about the wisdom of having cut rates and raises the prospect of rand and price volatility."
The bank also said that growth in the third quarter might cause a drop in overall output because of a surprisingly strong showing in the previous three months by the volatile mining sector, which accounts of 6 percent of output.
Mining grew by 31.2% from a 16.8% contraction in the first quarter, helping put GDP growth to 3.2%.
"The interpretation of GDP has to look at the base effect of mining, and that the non-primary sector of the economy has slowed down. The boost we got from mining may come to haunt us in the next quarter," said Rashad Cassim, the bank's head of research.
Mining dragged on growth in the first quarter after strikes led to a shutdown at a large Impala Platinum mine. Another platinum mine, owned by London-headquartered Lonmin, has been hit by a similar shutdown for the past month.
The bank cut its 2012 GDP forecast in July to 2.7 percent from 2.9 percent, while the finance minister has said he will cut his own forecast to below 2.7 percent in October. – Reuters