Great look at Apple Pay and what’s behind the secure payment system. Pretty in depth look with a lot of great info here.
With Apple Pay, no credit card data — even in encrypted form — is ever stored on the iPhone or on Apple’s servers. Similarly, no credit card data is ever transmitted to or stored on a merchant’s servers.
When a user first signs up for Apple Pay, either via an existing iTunes credit card or by loading a new one onto the iPhone, the card information is immediately encrypted and securely sent to the appropriate credit card network. Upon determining that the credit card account is valid, a token is sent back down to the device whereupon it’s safely stored within the iPhone’s Secure Element.