The ICC had a warrant for Bashir's arrest.
In a boost for the ICC, however, Adama Barrow, the new democratically elected president of the Gambia, recently reversed that decision - made by Yahya Jammeh, the west African state's former authoritarian leader.
Mojapelo added that government decisions must be based on "the expressed authority of the constitution".
Under the Rome Statute, South Africa as an ICC member has an obligation to arrest anyone sought by the tribunal.
The court ruled that the withdrawal was unconstitutional and invalid.
SA fell foul of the ICC in 2015 when it refused to detain Sudanese President Omar al-Bashir, who is wanted by the ICC for war crimes. However, the court's ruling could mean a significant delay in the process, and some legal experts speculate that the government might consider dropping its withdrawal plan ahead of the next presidential elections in 2019.
"Government will reflect on the reasons for the judgment and decide whether to appeal or not".
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But if the government is eventually forced to go to Parliament for approval, it can expect a bruising battle.
Under the rules of the court's treaty, a withdrawal does not take effect until a year after a notice has been submitted to the United Nations.
It's an important ruling for global justice both in South Africa and beyond.
"We really hope that this judgment does create breathing space for government to reconsider and perhaps to come up with a reasonable approach".
Three African states - South Africa, Gambia and Burundi - a year ago signalled their intention to quit the ICC. Shortly before the court ruling on Wednesday, parliament began asking for public submissions on the ICC issue.
As government deliberates on a damning court finding around another unconstitutional decision, this time related to the International Criminal Court (ICC), the ruling has been welcomed by some political parties as a victory for the rule of law.
South Africa said it was quitting the ICC because membership conflicted with diplomatic immunity laws. It stated that "South Africa does not want to be lumped together with pariah states who have no respect for human rights and who do not subscribe to accountability for those guilty of the most heinous human rights violations". Instead, the government should follow "the human rights-based foreign policy spearheaded by the late President Nelson Mandela".
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