The relatively immature eBook market endured some sharp growing pains yesterday as Apple forced the removal of in-app eBook markets from rival apps – Kobo, Kindle, Nook – in the App Store.

Users of those apps on iOS devices still will be able to read from their existing libraries –  they just won’t be able to purchase books from within the app.

The move comes as Apple seeks to protect its native iBooks business while also making good on enforcement of its policy set in stone back in June that app users could still read content purchased from external sources, so long as “purchase” buttons that led to third-party stores were removed.

Apple also has made law that any content available through in-app purchase must also be made available in the iTunes store, where it would be subject to the company’s 30/70 revenue split. The company had set a June 30 deadline for all publishers to comply with the rules, but yesterday was apparently judgment day.

Amazon, Barnes & Noble and Kobo have all removed their in-app stores from their apps as of today, while Google’s Google Books app was removed entirely from the App Store.