As far as we can tell, Apple Pay only supports purchase functions built-into native iOS apps (e.g., to buy upgrades/add-ons/tokens/etc. to use within the app itself) as well as making payments at real-world physical stores that have the equipment to accept Apple Pay. It does not appear to have any provision to process payments for general Web-based purchases, such as orders placed through any online shopping cart like E-junkie.
If they expand Apple Pay at any point to work with Web-based online purchases outside of iOS apps and physical stores, we'd certainly be interested in considering integration with it or, more likely, with a payment processor that supports it as a checkout method.
