Let’s take a look at the history of Arab Israelis within Israel proper. First, after the 1948 ethnic cleansing, the remaining Palestinian population within the new Israel were subject to Israel Martial Law and Defence (Emergency) Regulations, later practiced in the occupied territories after 1967.
Not nearly as brutal as Palestinians living in East Jerusalem, the West Bank, or Gaza, but they all live under Israeli Military Control. This is Apartheid, by international definitions.
Three main international treaties prohibit and/or explicitly criminalize apartheid: the International Convention on the Elimination of All Forms of Racial Discrimination (ICERD), the International Convention on the Suppression and Punishment of the Crime of Apartheid (Apartheid Convention) and the Rome Statute of the International Criminal Court (Rome Statute).
Amnesty lays this out very well in the first chapter of its report.