EMV tokenisation is a new standard that EMVco published this year[0], which allows the person holding the card details to generate an entirely new set of card details which are essentially aliased to the original card details. The result of all this is that Apple don't have to store the original card details.
However, the standard can allow for other things as well - it can allow for users to generate a new token per-merchant which could be used online or in person. Or merchants could generate a new token from a customer's card that'll only be usable with that merchant for storage, thus standardising what the likes of Stripe do while implementing a significant amount of backwards compatibility with the existing system.
[0] http://www.emvco.com/specifications.aspx?id=263
