In 2009 the South African Human Sciences Research Council found that Israel is practicing apartheid (and colonialism). This position was confirmed by the Russell Tribunal on Palestine, which sat in Cape Town in November
2011, and most recently, in March 2012, by the United Nations Committee for the Elimination of Racial Discrimination.

Israel is guilty of apartheid crimes not in comparison to what happened in South Africa, but in accordance to international law:

“…The inhuman acts … do not occur in random or isolated instances. They are sufficiently widespread, integrated and complementary to be described as systematic. They are also sufficiently rooted in law, public policy and formal institutions to be described as institutionalised.

[…]

Israel must cease its apartheid acts and its policies of persecution and offer appropriate assurances and guarantees of non-repetition. In addition, Israel must make full reparation for the injuries caused by its internationally wrongful acts, with regard to any damage, whether material or moral. With regard to reparation, Israel must compensate the Palestinians for the damage it has caused, with compensation to cover any financially assessable damage for loss of life, property, and loss of profits insofar as this can be established.

States and international organisations also have international responsibilities. They have a duty to cooperate bring Israel’s apartheid acts and policies of persecution to an end, including by not rendering aid or assistance to Israel and not recognising the illegal situation arising from its acts. They must bring to an end Israel’s infringements of international criminal law through the prosecution of international crimes, including the crimes of apartheid and persecution.”

Quoted from:
Russell Tribunal on Palestine.  Cape Town Session. 2011. Summary of findings [Online].

Read the full findings here: RToP Cape Town full findings