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