I may be missing something here but you are paying VAT on the amounts that you invoice your clients, unless you have VAT inclusive expenses then it will not affect that bottom line?
Without getting too technical and involving IT and other factors, here is a simple example:
Client pays you R1150 as per your invoice. You owe SARS the VAT portion of R150, included is the referral fee that you need to pay to a non-vendor so you cannot claim that VAT portion of this fee back as an expense?
1150 Income received
- 250 Referral fee
- 150 VAT portion
= 750
You made R750, it really does not matter whether this R250 was included in the invoiced amount or if you had to pay it out separately.
This said, if you had to pay the R250 out separately to a VAT vendor, you could claim the VAT portion of that expense back which means you would actually come out with R32.61 more.