Originally Posted by
skywardhunter
It might be an issue, security and immigration can be a little tough in the morning around 8-9am.
Customs won't care, you might be more concerned with immigration, but I doubt they'd care, either.
You do not say when you are travelling, but bear in mind that we are going into Winter, so that means a rainy season in Cape Town. This of course, could lead to early morning flight delays, so maybe look at a slightly earlier CPT- JNB departure just to be on the safe side.
If you are travelling on one ticket, (Oneworld), you should be able to check your bags all the way through, and as mentioned, Immigration just bumbles along, so they do not care about the length of your stay.