The public international law prohibition of apartheid is best found in an advisory opinion by the International Court of Justice relating to South Africa’s presence in Namibia (Namibia case), where the violation is defined as “distinctions, exclusions, restrictions and limitations exclusively based on grounds of race, colour, descent or national or ethnic origin which constitute a denial of fundamental human rights”.
130. It is undisputed, and is amply supported by documents annexed to South Africa's written statement in these proceedings, that the official governmental policy pursued by South Africa in Namibia is to achieve a complete physical separation of races and ethnic groups in separate areas within the Territory. ...
131. Under the Charter of the United Nations, the former Mandatory had pledged itself to observe and respect, in a territory having an international status, human rights and fundamental freedoms for all without distinction as to race. To establish instead, and to enforce, distinctions, exclusions, restrictions and limitations exclusively based on grounds of race, colour, descent or national or ethnic origin which constitute a denial of fundamental human rights is a flagrant violation of the purposes and principles of the Charter.
International law did not define the crime of apartheid in 1971. This ruling did not try to define apartheid in any sense. South Africa freely admitted it had a policy of apartheid. The entire question before the IJC was whether South Africa's policies in Namibia were a violation of the UN Charter.
Just like HRW, Amnesty realized that the definitions of apartheid under international law do not apply to Israel, so they must grab whatever half-truths they can find and claim that the Frankenstein monster of connecting parts from the Rome Statute, the Apartheid Convention (which only say "racial discrimination" similar to that of South Africa), the ICERD (which excludes non-citizens from its expanded definition of "racial discrimination,") and now the ICJ Namibia Case (which does not define apartheid nor racial discrimination in any sense.)
Amnesty is lying - and they know it.