This is such a baseless and inflammatory mischaracterization. It's like the tamer version of those who have unironically compared mask and vaccine mandates to the persecution of Jews in Nazi Germany.
No one is being forcibly vaccinated so arguments about "body autonomy" are completely irrelevant. It's just that not getting vaccinated has consequences and people don't like there being negative consequences to their (irrational) actions.
You need to have a bunch of vaccines to attend public schools in most places. This is nothing new.
Yet people lose their shit because they're told to wear a mask on a plane when that policy was known before they even bought the ticket.
To characterize any of this "apartheid", just like the comparisons to Jewish persecution in Nazi Germany, belies an ignorance and diminishes the suffering of black South Africans in Apartheid.