Israel never supported apartheid, they condemned that policy and only reluctantly worked with South Africa on tech-sharing (especially in regards to nuclear weapons) and economic terms because they needed some allies outside of Europe and North America. South Africa and Rhodesia were last-choice picks from who they could work with in Africa, because the only black African states at the time willing to work with Israel were Malawi and Ethiopia (pre-collapse of its monarchy).

There's no official stats on Israeli thoughts on apartheid that I've seen but most of the sources I've read on the subject usually said the Israeli population didn't really like the South African government and Apartheid.

The article on South Africa-Israel relations on Wikipedia and this article here have a lot of good information about the subject.