The idea behind PayFast is to speed up ecommerce fulfilment through positive acknowledgment of funds received. There is also a reduction in admin overhead for the seller in terms of not requiring proof of payment, not doing manual reconciliation, etc.
The intention too, is that PayFast collects multiple payments on behalf of a receiver and then pays the receiver in bulk at the receiver's request.
Funds received are accumulated to your PayFast account from where you request a Payout on a regular basis (eg. weekly) to have the funds transferred to your bank account.
For fraud prevention and security purposes, each payment is subject to a withdraw delay (shown on your PayFast dashboard) so your received payment will only be available after the indicated duration has passed (48 hours).
You can continue with the fulfilment of the order safe in the knowledge that the funds have been received and credited to your PayFast account and will shortly be available to be transferred to your bank account.