South Africa has long been a vocal supporter of the Palestinian cause, with the ruling African National Congress (ANC) often linking it to its own struggle against apartheid.
Foreign Minister Naledi Pandor said the recall of the diplomats was "normal practice", adding the envoys would give a "full briefing" to the government, which will then decide whether it can be of assistance or if a "continued relationship is actually able to be sustained".
"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," Pandor told a press conference on Monday, as she hosted her Ukrainian counterpart Dmytro Kuleba.
Earlier, Ntshavheni accused Israeli ambassador Eliav Belotserkovsky, of making derogatory comments about South Africans, including members of government, "who are speaking against the holocaust being committed by the Israeli government".
The foreign ministry had been instructed "to convey the South African government displeasure with the ambassador" through diplomatic channels, she said.
"We felt it important that we should call the ambassador in," added Pandor.
"There seems to be a strange practice among some ambassadors in South Africa, that they can just say what they like... I don't know if it's because it's an African country and they disrespect us but it's something that we should not tolerate," she said.
Last month, Pandor denied she had expressed support for Hamas's October 7 attack in a phone call with the group's leader, which she said had focused instead on humanitarian aid.
Numerous pro-Palestinian protests have taken place across South Africa over the past month.
President Cyril Ramaphosa is among several ANC officials who have participated sporting flags and keffiyeh scarves, in a show of solidarity with the Palestinians.
Home to the largest Jewish community in Sub-Saharan Africa, the country has also seen several pro-Israel demonstrations and initiatives, including the setting-up in Johannesburg of a Shabbat dinner table with empty chairs and photos of the hostages held by Hamas.
