I'm sorry, but I'm failing to see how IBM actively facilitated anything other than being able to more effectively process information on citizens - something that most modern countries either already have or very strongly desire.

the national identification system was highly
customized, requiring close collaboration with the
South African government;

So are most IBM products on a large scale. This is no different from how IBM typically treats all of its high-paying customers, including large-scale enterprises and - you guessed it - governments.

Now granted, IBM probably shouldn't have been doing business with the South Africans in the first place, customizations or no. However, IBM wanting to create a customized system for the specific needs of a major customer is not out-of-the-ordinary by any means, nor is it any reason to be up-in-arms.

racial classification was a primary identifying
characteristic;

Racial classification is a significant identifying characteristic in virtually all citizen databases, censuses, etc. You'd be hard-pressed to find a country whose census doesn't at least mention race or ethnicity. I will, however, concede that incorporating race in the identification number itself - as the South Africans did - is highly suspect, but it's not stated whether or not IBM was the one that actually implemented that aspect of the identification system in question.

and the equipment was leased.

What does this have to do with anything?

The EFF article is trying to claim that - by the mere merit of IBM having helped South Africa develop a citizen identification system - it's complicit in human rights violations. Guess what? There exists a staggeringly-large quantity of countries with citizen identification systems[0]. It would be one thing if IBM designed the system specifically for the purpose of discriminating against blacks, but this article hasn't really made a convincing argument of that (namely, it hasn't provided any real proof that enabling apartheid was indeed IBM's goal). As far as I can tell, IBM was simply helping South Africa develop the same sort of system that most other countries either already had or would soon have. In other words, IBM's involvement was to implement a general-purpose product which was then subsequently abused by the South African government.

I will admit that the implementation of a race code in the identification numbers themselves is suspect, and perhaps that's what the EFF is going after (if IBM was indeed involved in that particular element of South African citizen ID numbers; the article doesn't really go into detail on that). It's also suspect that IBM proceeded with this (according to the EFF, at least) after having been disallowed from doing so by the U.S. government, and that IBM was secretive about it. However, the act of creating an identification system - on its own - does not seem as if it can be classified as "directly facilitating" anything, let alone racism. The EFF would have a better case if they focused on those individual elements rather than trying to claim that the ID system in its entirety was designed to facilitate that institutionalized racism.

This is all not to mention that IBM actually has a very positive track record for eschewing racial discrimination in its hiring decisions and workplace environments[1]; creating something specifically to oppress a particular racial demographic is quite a bit out-of-character for them.

[0]: https://en.wikipedia.org/wiki/National_identification_number

[1]: https://en.wikipedia.org/wiki/IBM#Work_environment