The court ordered Israel to prevent acts of genocide against the Palestinians and do more to help civilians, as it wages war against Hamas militants in the Gaza Strip.
It has not yet ruled on the core of the case brought by South Africa - whether genocide has occurred in Gaza.
Israel has called South Africa's allegations false and "grossly distorted", and said it makes the utmost efforts to avoid civilian casualties.
"Today marks a decisive victory for the international rule of law and a significant milestone in the search for justice for the Palestinian people," South Africa's department of international relations and cooperation said in a statement.
"South Africa sincerely hopes that Israel will not act to frustrate the application of this Order, as it has publicly threatened to do, but that it will instead act to comply with it fully, as it is bound to do."
It said South Africa would continue to act within the institutions of global governance to protect the rights of Palestinians in Gaza.
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