Both numbers come from SARS and both have 10 digits, so they are easy to mix up. Only one of them proves a supplier is registered for VAT. Here is how to tell them apart.
SARS gives a business several reference numbers. The two that get confused most often are the VAT registration number and the income tax reference number, because both are 10 digits long and both appear on SARS correspondence.
They do different jobs. The income tax reference number identifies a taxpayer for income tax. The VAT registration number shows that the business is registered as a VAT vendor, and it is the number that belongs on a tax invoice and that you look up to confirm VAT registration.
A typical route is a supplier form with a single field labelled "tax number". The supplier fills in its income tax reference, and the accounts team captures it as the VAT number. Because it has the right length, it passes a visual check, and it can sit in the vendor master for years.
The cost shows up later: input tax claims backed by a number that does not prove VAT registration, and a supplier that may not be registered for VAT at all. Only a lookup against the SARS VAT vendor search reveals the problem, because the number looks plausible on paper.
Start with the cheap filter. Export the VAT number field from your accounting system and sort it: anything blank, anything that is not 10 digits, and anything that does not start with 4 is not a VAT number and needs a conversation with the supplier.
Then check the rest. A number can pass the format filter and still be wrong, because the supplier has deregistered or two digits were swapped when it was captured. Running the remaining numbers through the bulk SARS VAT vendor search shows which ones SARS actually finds, and gives you an exportable record of the clean-up.
No. Only businesses registered for VAT have a VAT number. Most taxpayers have an income tax reference number, but that says nothing about VAT registration.
No. The SARS VAT vendor search looks up VAT registration numbers. An income tax reference number will not be found there, even for a business that is registered for VAT.
No. The CIPC number identifies the company in the companies register. VAT registration is separate and is shown by the VAT number SARS issues.
On the notice of VAT registration SARS sent when the business registered, and on your SARS eFiling profile. It is the 10-digit number starting with 4 that should appear on every tax invoice you issue.