Local communities and environmental groups had challenged the seismic survey plans, arguing in part that they had not been adequately consulted.
Justice Jody Kollapen said the Supreme Court of Appeal’s order was set aside.
Shell said it remained committed to responsible offshore exploration, stakeholder engagement and environmental stewardship.
The ruling does not affect Shell’s broader exploration plans in South Africa.
Shell received environmental authorisation last year to drill up to five ultra-deepwater exploration wells in the Northern Cape Ultra Deep Block off South Africa’s west coast, part of the Orange Basin, which extends north into Namibia.
Shell has made several major discoveries on the Namibian side of the basin, where exploration has advanced more rapidly.
The company is also pursuing a 60% operating interest in South Africa’s Block 2C through a proposed farm-in agreement with state-owned PetroSA.
Under the proposed deal, Shell would pay a $25 million signing bonus and fund about $135 million to $150 million for an initial three-well programme.
The transfer remains subject to regulatory approval.
South Africa’s offshore acreage lies alongside the Orange Basin, one of the world’s most closely watched emerging oil and gas exploration regions.
However, legal challenges and permitting disputes have repeatedly delayed exploration activity on the South African side of the basin.
Shell has meanwhile been reducing its downstream exposure in South Africa while continuing to pursue upstream opportunities.
The company has moved to sell its South African retail and trading business after previously disposing of its stake in the shuttered Sapref refinery.
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