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From your phone's lock screen, you can double tap the home button to launch Apple Pay. Then you can enter your fingerprint so it's activated and ready to go when you get to the checkout.
In the current version of iOS, Apple Pay only activates when you tap your iPhone against a special near-field communication (NFC) reader that's compatible with the service. The new system in iOS 9 will save you an extra step.
It's also similar to the way Apple Pay works on the Apple Watch.
Since the Apple Watch remains authenticated after you strap it on and put in your passcode, all you have to do is double click the button on the side to arm Apple Pay.
iOS 9 will be available as a free download for most iPhones and iPads in the fall.