The Department of International Relations and Cooperation (Dirco) has denied that it offered support to Hamas.
It said Minister Naledi Pandor had received a call to talk to the leader of Hamas, Ismail Haniyeh, about the humanitarian corridors in the besieged Gaza Strip following the persistent bombing and cutting off of food, electricity, and water supplies by the Israeli government.
The department said Pandor spoke to Haniyeh about these issues.
It insisted that the discussions were never about support for Hamas.
The discussions focused on sending food, medicine, water, fuel, and electricity to the people of Gaza.
"The reports that Minister Pandor also offered support for the 'Battle of Al-Aqsa Flood' are untrue and meant to impugn the Minister and the government of South Africa.
"Minister Pandor's call with the Hamas leader is in line with South Africa's readiness to engage all interlocutors as part of facilitating dialogue to end the ongoing conflict," said the department.
"South Africa therefore calls on all sides to seize the opportunity for peace as opposed to violence and for the international community to actively advocate for the implementation of its own international resolutions and establish a credible peace process.
"South Africa stands ready to share its experience in mediation and conflict resolution as it has done on the continent and around the world," said the department of international relations.
President Cyril Ramaphosa has from last week, when the conflict began, has been offering to mediate between the warring parties.
He said South Africa has been involved in mediation in the past in global conflicts.