New Apple App Store rules took affect today, possibly leading the way to a showdown between eBook retailers and Apple.

MacRumors quoted the new Apple App Store rule:  “Apps can read or play approved content (specifically magazines, newspapers, books, audio, music, and video) that is subscribed to or purchased outside of the app, as long as there is no button or external link in the app to purchase the approved content. Apple will not receive any portion of the revenues for approved content that is subscribed to or purchased outside of the app.”

As you can see by the screenshot from Amazon’s iPhone app this afternoon, the Kindle app still links to Amazon’s eBookstore–possibly breaking the “external link in the app to purchase” rule. Both companies have kept quiet about the potential showdown. What do you think will happen?