A few details to be considered:
Both are good for secure credit card purchases in and outside of RSA in Rand.
The difference is that PayFast is local and we know them well (support), their transaction fees are lower – about 3,7% per transaction.
On the surface people might think Paypal is cheaper, but the real costs are hidden behind "cross border" fees, FNB's added margin etc... such that the total cost can be up to 9% per transaction.
PayPal – collects the money in Rand but converts into Dollars (you get paid out in $ which you need to convert back into rand) and the fees are therefore currency conversion rate-dependant.
The invoices always come from the Shopstar system in Rand (or the shop currency).
Some shops offer both, but we recommend to use PayFast if you mostly do business within RSA.