This is due to solid growth in the agriculture and financial industries outweighed a hammering in the strike-hit mining sector, data showed on Tuesday.
Africa's most developed economy is struggling to right itself after waves of labour unrest this year hit corporate confidence, while rising food and fuel prices have squeezed consumers.
The economy grew 0.6 per cent in the second quarter after contracting by the same amount in the first three months of this year, Statistics South Africa said on Tuesday. A Reuters poll of 26 analysts had forecast growth of 0.9 per cent.
On an unadjusted year-on-year basis, the economy grew by 1 per cent in the second quarter, compared with growth of 1.6 per cent in the previous three months.
Analysts had expected year-on-year growth of 1.2 per cent.
"We should remember the level of growth seen today is exceptionally low and totally insufficient to solve South Africa's deep developmental and jobs problems," Peter Attard Montalto, an emerging markets analyst at Nomura International, said in a note to clients.
The mining and quarrying industry saw a 9.4 per cent drop in quarter-on-quarter output, the data showed, after being hit by a five-month platinum strike this year.
Manufacturing, the economy's second-largest sector, fell by 2.1 per cent from the previous three months, reflecting weak demand from struggling consumers.
(WATCH VIDEO: Subdued recovery expected for Manufacturing sector)
Agriculture grew up nearly 5 per cent, while finance and real estate expanded by 1.5 per cent, the data showed.