And, apparently, at "card present" transaction rates, which I imagine took some degree of negotiation on Apple's part.
http://bankinnovation.net/2014/09/apple-said-to-negotiate-de...
http://bankinnovation.net/2014/09/apple-said-to-negotiate-de...
When the payment is processed, that same network/bank takes the token provided, translates it back to a card number and passes the card number to the issuing bank.
I think it's actually quite a feat that Apple managed to tokenize all 800 million existing card numbers, because of this requirement.