The protesters gathered at the entrance of the OR Tambo Building in Pretoria, the headquarters of the department of international relations, calling for the expulsion of the Israeli ambassador.
More than 200 activists lined the busy Soutpansberg Road chanting, “Free Palestine”.
Some shouted: “Down with Israeli apartheid, down” waving flags and placards.
International media reports on Friday afternoon said two more Palestinians were killed, raising the death toll in four days to 100.
On Thursday, the African National Congress described the Israeli military’s attacks on the Gaza strip as “barbaric”.
“The state of Israel has turned the occupied territories of Palestine into permanent death camps,” deputy secretary general Jessie Duarte said in a statement.
“Of course the killing of any child, irrespective of race, colour or creed, must be condemned and the death of [three] Israeli young people is surely as senseless as any other death.”
However, the killing needed to stop, she said.
Three Israeli teenagers — Naftali Fraenkel, 16, Gilad Shaer, 16 and Eyal Yifrah, 19 — were kidnapped and murdered last month.
Agence France-Presse (AFP) at the time reported that the three disappeared from a popular hitch-hiking spot near the southern West Bank Gush Etzion settlement late on June 12.
The Israeli military found the teenagers’ bodies in a field northwest of Hebron on June 30.
On July 2, 16-year-old Palestinian teenager Mohammed Abu Khdeir was burnt to death.
This reportedly triggered days of clashes in east Jerusalem and Arab Israeli towns.
Scores of people have died during the Gaza raids and Israel’s Operation Protective Edge, launched early on Tuesday to stop rocket fire reportedly by Hamas militants.
The SA Jewish Board of Deputies and the SA Zionist Federation condemned Duarte’s statement.