How will it work? We can’t be 100% sure of the specifics, but we can imagine that when making purchases online, websites will have the option of allowing users to pay via Apple Pay. When that option is selected, users will then be prompted on their mobile devices to authenticate the payment/purchase via Touch ID.
In a way you could think of Apple Pay for websites as being similar to using Touch ID to verify your identity when purchasing apps in the iTunes App Store, or how banks provide users with dongles or SMS two-factor authentication to verify that customers are who they say they are. Of course this implementation will require websites to hop on board the Apple Pay bandwagon.
However given that this probably won’t require retailers to install/purchase new hardware, adoption should be easier (we think). In any case hopefully the details will be revealed at WWDC so check back with us next week for more updates.