Did they have separate facilities for blacks and whites during apartheid?

There were indeed separate facilities for the races under apartheid, thanks to a notorious piece of legislation called the Reservation of Separate Amenities Act of 1953. In most parts of South Africa, facilities had already been unofficially segregated for some tine. What the Act did, then, was to codify existing cultural practices, putting them on an explicitly legal footing.
Under the Act, a wide variety of amenities were racially segregated, such as beaches, buses, and even public parks. Unlike the racist state governments of America's Deep South, the authorities in apartheid-era South Africa made no pretense that separate facilities were equal. This was because there was no legal precedent to this effect. The minority white government believed that white people were inherently superior and deserved better treatment.
Some facilities, such as public roads, were exempt from the Act, but this was only for practical reasons. The authorities expected black people to work, and segregating public roads would have made that virtually impossible. Nonetheless, public transport was segregated, with the black majority having to endure vastly inferior services compared to their white counterparts.