Hlongwane and Thuzi also scored six distinctions - Mathematics, Physical Science, Accounting, English, Life Orientation and Geography.
Thuzi just missed a seventh distinction in IsiZulu by a single mark.
Chikonye and Thuzi are heading to the University of Cape Town, while Hlongwane will study at Wits University.
The three best friends will all be studying Actuarial Science.
Chikonye said: I can t believe that I am the third-best pupil in Physical Science nationally. I dedicate this milestone to my schoolmates, parents, siblings and teachers for all their hard work and positive messages. Many people believed in me. I was optimistic that we were going to raise the flag of our school higher than before. We are now going to begin new lives away from our families and teachers. We are going to make them happier by reaching more goals in future.