Yes. Most notably in the Battle of Cuito Cuanavale, 1987-1988, which is said by many to be the biggest battle in Africa since WW2 (but the same thing is also said about the Battle of Afabet, 1988, in the Ethiopian Civil War). At the peak, there were about 3000 Cubans and 3000 South Africans on their respective sides in the battle.

There are a number of books devoted to the battle, and many more wesbites (it's attracted a lot of attention, partly due to the Cuba vs South Africa component). Be warned: a lot of the discussion is politicised and propagandised. Both sides claimed victory in the battle, and overinflated claims of enemy casualties are common.

A good balanced account is Edward George, The Cuban Intervention in Angola, 1965-1991 (Routledge, 2012).

The Battle of Cuito Cuanavale wasn't the only fighting involving both Cuban and South African forces, but it's the best known and the most written about. Also the largest battle involving them. Both Cuba and South Africa had military forces in Angola in the 1960s, during the independence war against the Portuguese, so they were on opposing sides of 20 years of warfare in Angola.