NEW YORK — Visa, MasterCard, and major banks agreed to pay retailers at least $6 billion to settle a long-running lawsuit that alleged the card issuers conspired to fix the fees that stores pay to accept credit cards. As part of the settlement, disclosed late Friday, stores will be allowed to charge customers more if they pay using a credit card.

The pact, which is being called by lawyers involved in the case the largest antitrust settlement in US history, is seen as a major victory for merchants that have long complained about the billions of dollars in so-called swipe or interchange fees that they pay to banks for each purchase made using plastic. But at a time when shoppers increasingly are using credit and debit cards, merchants face the dilemma of how to charge shoppers extra without angering them.

‘‘These new rules will give merchants the tools they need to put pressure on the credit card networks to lower interchange or swipe fees, which are the second- or third-highest cost of doing business for many retailers,’’ said Patrick J. Coughlin, one of the lawyers for the plaintiffs.

According to the National Retail Federation, the nation’s largest retail group, credit card swipe fees cost retailers about $30 billion per year. Duncan Mallory, senior vice president and general counsel for the group, said the settlement is a step in the right direction.

The dispute dates back to 2005 when large retailers filed price-fixing lawsuits against Visa, MasterCard, and other banks. The retailers claimed the credit card issuers conspired to fix the fees that stores pay to accept credit and debit cards.

The card companies long have long defended the fees. They say stores benefit from being able to accept credit and debit cards from customers. Visa and MasterCard have banned stores from charging customers more for purchases customers make with credit cards. But merchants are allowed to offer customers discounts if they pay with cash. Some gas stations do this, for example.