Minister in the Presidency Collins Chabane said the executive had approved a report drawn up by the task team established to explore the controversial means of extracting gas from shale rock formations deep underground.
The security of energy supply to South Africa had been an important consideration in Cabinet's decision, Chabane told the media on Friday.
South Africa was "an energy scarce country" and the possibility of discovering a resource like shale gas could alleviate the energy challenges facing the country, he said.
The task team had deemed that it was "clearly safe to start a programme of exploration for shale".
Chabane indicated that the task team's report and its recommendations would be made public, in line with a similar commitment made by the Minister of Mineral Resources Susan Shabangu.
Fracking was deemed to pose a potential threat to South Africa's participation in the construction of the world's largest radio telescope the square kilometre array (SKA).
The report recommended a buffer zone be set up between the area earmarked for the SKA, and where fracking exploration will be permitted.
This buffer zone was sufficient, according to scientists, to ensure that neither operations would be negatively affected, he said.
Chabane gave assurances that environmental concerns, a chief reason for vocal objections to fracking in the Karoo, would be addressed through the environmental authorisations required by law before exploration began.
Fracking uses a mixture of sand, chemicals and vast quantities of water to release the gas trapped underground. Critics fear that the process will contaminate water supplies in an already dry area and damage air quality.
The department of mineral resources is expected to provide a detailed briefing on the issue early next week.
A number of gas and oil companies, including Shell, Falcon Gas and Oil and Sasol had applied for prospecting rights over areas of the Karoo when the department of mineral resources instituted the moratorium last year.
The Cabinet mandated Shabangu to begin a process of public consultations with interested and affected parties to provide further details, following the cancelling of the moratorium.
Gas is seen by many, notably the country's National Planning Commission, as a means to bridge South Africa's electricity supply shortages.
It can fuel power plants that are faster to build and bring online than large baseload power stations, such as nuclear power plants or mega coal fired operations, such as Eskom's new Medupi and Kusile stations, currently under construction. A secure domestic supply of gas would also ensure a cheaper, more reliable fuel source.
During its lekgotla, the Cabinet also endorsed the National Development Plan written up by the NPC and adopted by Parliament last month.
The NDP strongly cautions against plans to expand South Africa's nuclear power base, without a more thorough cost benefit analysis.
The department of energy's 20-year plan for electricity, known as the integrated resource plan, makes allowance for the addition of 9600MW of nuclear generated power.
Chabane said that with the adoption of the NDP government would have to now begin to "readjust" its work to align with the NDP. This included he noted the readjustment of government departments' sectoral plans, such as the energy department and its integrated resource plan.