Paying a contractor looks like paying any other supplier, and mostly it is. The exceptions are the ones that cause trouble, and they are worth knowing before the first invoice rather than at year end.
Get a proper invoice
Their registered or trading name, their tax number, an invoice number, the date, a description of what was supplied, and the amount — with VAT shown separately if they are registered.
A payment made against a WhatsApp message is a payment you may struggle to claim as an expense. Where a contractor cannot produce a proper invoice, that is worth noticing for what it says about how they run their own business.
Check whether they are VAT registered
If they are, they charge it and you claim it back where you are registered yourself. If they are not, they must not charge it — and an invoice showing VAT from somebody who is not registered is a problem for both of you.
Ask for the VAT number and keep it on file. It is a thirty-second check that occasionally saves a disallowed claim.
Withholding
Generally you do not deduct employees' tax from a genuine independent contractor — they account for their own. That is precisely why classification matters: if the person is actually an employee, the tax you did not deduct becomes your liability.
There are specific situations where withholding does apply, particularly with payments to non-residents, where an obligation can fall on the payer. If you are paying somebody outside the country, check the position before paying rather than after.
Pay the business, not the person
Where a contractor trades through a company, pay the company's account, against the company's invoice. Paying an individual's personal account for work invoiced by an entity creates a mismatch your accountant will have to explain and which muddies the classification question.
Pay on the agreed terms
Contractors are small businesses with the same cash flow problem you have, and they are usually carrying the cost of the work until you pay. A client who pays on time is worth more to a good contractor than one who pays slightly better and slowly.
If you cannot pay on the date, say so before it rather than after. That single habit determines whether the people you like working with stay available to you.
Keep the records together
The agreement, the invoices, proof of payment, and their tax and VAT details. That set supports the expense claim, supports the classification if it is ever examined, and answers most of what an accountant or an auditor will ask.
Filed as you go, it is nothing. Assembled a year later from bank statements, it is a day's work and an incomplete picture.
General guidance, not tax or legal advice. Withholding obligations, particularly on cross-border payments, are specific and change; confirm with SARS or a registered tax practitioner.