Earlier quoted context omitted.
My understanding is that, once you're a citizen of Israel, you have the same rights as other Israeli citizens, regardless of race or religion. Under apartheid, rights were infringed based on race.
I see the distinction here. In South Africa you could be a citizen regardless of your race, but how you were treated depended on your race; citizens were not equal. In Israel, they are trying to prevent people of a certain race from becoming citizens, but once you are a citizen, there are fewer 'official' racist policies even if a lot of the people you have to deal with are outwardly racist anyway. On paper, citizens…
You can make an analogy to apartheid. It's up to others to determine if the analogy fits the point you are making though.