Penguin offered in April to end "most-favoured nation" contracts for five years. Such clauses bar rival retailers from selling ebooks more cheaply than Apple.
It also proposed to let retailers set prices or discounts for a period of two years. The concessions are similar to those offered by four other publishers last year.
The European Commission said the publishers' offer would boost the ebook market.
"After our decision of December 2012, the commitments are now legally binding on Apple and all five publishers including Penguin, restoring a competitive environment in the market for ebooks," European Competition Commissioner Joaquin Almunia said in a statement.
© Thomson Reuters 2013
For the latest tech news and reviews, follow Gadgets 360 on X, Facebook, WhatsApp, Threads and Google News. For the latest videos on gadgets and tech, subscribe to our YouTube channel. If you want to know everything about top influencers, follow our in-house Who'sThat360 on Instagram and YouTube.