The officials
These are two different officials concerned with patent registrations.
The Registrar of Patents deals with the applications for registration of a patent and most things concerning the application up to registration. Technically, the Patents Office is within CIPC, itself a branch of the Department of Trade, Industry and Competition. The day-to-day functions of the Registrar are executed by CIPC officials, and there is indeed a head of that office titled the Registrar of Patents.
Read section 7 of the Patents Act.
There is also the Commissioner of Patents. Technically, he has no connection to the Registrar and is actually a judge of the High Court who decides court cases involving patents. Typically, such cases concern infringement or cancelling (revoking) a patent.
Read sections 8, 17–19 of the Patents Act.
Accordingly, when reference is made to the Registrar, it will be in connection with the registration procedure, renewal of the registration, and so on. When reference is made to the Commissioner, it means there is litigation brewing, or on the go.