[1] https://en.wikipedia.org/wiki/Hazaras
I have personally seen discrimination in Pakistan, by the ruling elite class in the Islamabad/Lahore area, against darker skinned persons of different ethnic groups whose home area is in Balochistan.
It just goes to show you that people like having power over other people, and they'll find any excuse possible to turn some group into the "other" so they can feel justified in oppressing them. In the case of the Indian caste system, race isn't required for this. In Afghanistan, as you point out, it can have a big religious component (though race is part of it too).
It is interesting to note that systematic racism against white people doesn't seem that common, at least in places I've visited (mostly Asia), where white people are in the minority. Discrimination there seems to be more xenophobia-based than race-based.