While addressing a press briefing, Khumbudzo Ntshavheni, a minister in the president's office, said all diplomatic staff in Tel Aviv would be asked back to Pretoria for consultations, without providing further details.
Ntshayheni's sentiments were re-iterated by Foreign Minister Naledi Pandor.
Speaking during a press conference, Pandor said, "we are... extremely concerned at the continued killing of children and innocent civilians in the Palestinian territories and we believe the nature of response by Israel has become one of collective punishment."
"We felt it important that we do signal the concern of South Africa while continuing to call for a comprehensive cessation (of hostilities)," Pandor added.
The recall of the diplomats was "normal practice," Pandor said, adding the envoys would give a "full briefing" on the situation to the government, which will then decide whether it can be of assistance or if a "continued relationship is actually able to be sustained."
Fighting has raged in the Gaza Strip for about a month since Hamas militants launched an unprecedented attack over the border from the territory into Israel on October 7.
Israeli authorities report over 1,400 people, most of them civilians, have been killed in the Middle Eastern nation since the attack, during which Hamas took more than 240 people as hostages.
In response, Israel has relentlessly bombarded Gaza and sent in ground troops, with the health ministry in the Hamas-run Palestinian territory saying more than 9,700 people have been killed, also mainly civilians.
President Cyril Ramaphosa's administration has been a vocal supporter of the Palestinian cause, with the ruling African National Congress, ANC, often linking it to its own struggle against apartheid.