BRUSSELS--European Union regulators Wednesday accepted an offer from Visa Europe to cap its interbank fees to the same level as MasterCard Inc.'s to settle an antitrust probe.

Europe's largest card payments company will cut the fees it charges retailers to 0.3% of the value of each transaction, a reduction of between 40% and 60%, the European Commission said. Rival MasterCard Inc. agreed to cap fees at that same level in 2009.

Visa Europe made the offer last year to cut the so-called Multilateral Interchange Fees, which are paid by retailers' banks to cardholders' banks and are fixed jointly by the retailers' banks.

Visa Europe is owned and operated by more than 3,000 European financial institutions and has a 40% market share in the credit and debit card market in Europe. More than 5 million merchants accept its cards.

The commitments "are excellent news for European consumers, since the fees paid by retailers end up on their bills," said the EU's antitrust chief, Joaquín Almunia.

Visa Europe said the agreement would provide "legal certainty" and would enable the company to "focus on developing and providing payment solutions for the benefit of consumers, rather than pursuing lengthy legal cases."

As part of its agreement with the commission, the firm agreed to reduce interbank fees for cross-border transactions to 0.3% for credit and 0.2% for debit transactions. It will also simplify its interbank fee structure and make the invoicing of card acceptance services more transparent to merchants.

The commitments are legally binding on Visa for four years and come nearly five years after the EU's antitrust watchdog filed a formal complaint against the company.

Visa Europe has undertaken to observe the proposed commitments for four years.

The European Commission said it is continuing proceedings against Visa Inc. in relation to its international interbank fees, which are fees that apply when a cardholder from outside the Visa Europe territory, such as the U.S., uses a Visa credit card to make a purchase in Europe.

Even though they share a brand, Visa Inc. and Visa Europe are separate entities that run their own clearance systems. The European firm is owned by financial institutions and operates as a licensee of New York-listed Visa Inc. Visa Europe is a minority stockholder in Visa Inc., and the U.S. company receives royalties from Europe.

MasterCard was told by European regulators to cap its fees in 2007 on the grounds that they were too high and flouted competition rules. MasterCard subsequently challenged that decision, which was upheld by the EU's General Court, the bloc's second highest court, in 2012.

Marcin Sobczyk, Andrew R. Johnson and Dana Cimilluca contributed to this article.

Write to Vanessa Mock at vanessa.mock@wsj.com

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