This is an interesting question, and one regarding which many disparate views exist. For an agreement to be validly signed under South African law it depends on the formalities relating to signing rather than the ink colour used. Unless the parties to the agreement intended some particular form of signature, any sign by placing a thumb print, printing your name or initials and in cases of an illiterate person by marking with a properly authenticated mark, made with the intention of signifying assent to the agreement will be sufficient.
As regards to the colour of the ink used to sign with, there is no legal requirement for a certain ink colour to be used. The colour of the pen is not relevant as it is only required to prove the necessary signatures. That said, over time a large degree of preference and common practice has developed, firstly preferring black ink, and these days increasingly also blue ink. Black ink is still the most used because it tends not to fade as quickly as other ink colours. Blue is also gaining in preference as it makes the signature stand out more clearly to differentiate an original from a scan or copied document. Other colours such as green and red can also be used, but generally fade faster which can cause problems if a document is intended to last for a long time. These colours also do not photocopy as clearly as black or blue ink.
So, whether you use black, blue or red it does not matter or affect the validity of the agreement so long as it has been properly signed and executed in accordance with the required formalities.