Here are a few links to register for 3D secure, depending who you bank with.
ABSA
Standard Bank
Nedbank
If you bank with FNB you can register for 3D Secure by doing the following on the FNB website (logged in).
Select the "My Bank Accounts" tab
Then select the "My Cards" tab
Find the card you want to activate
Click on the "Activate Now" link in the "Verified by Visa" column
Fill in all your details as prompted
You will be sent an OTP to your mobile phone - enter this in the OTP field
Once done, your card will be good-to-go for your next online purchase