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Visa Inc. and MasterCard Inc. agreed to pay scores of retailers more than $6 billion to settle a long-running lawsuit in an agreement that also permits merchants to charge higher prices to customers who pay for purchases with credit cards.

The settlement is expected to have wide-ranging implications for consumers, retailers and the card industry. It is also the latest victory for merchants, who have recently logged some significant wins in their efforts to reduce their cost of accepting plastic.

The agreement, which was reached after months of negotiations, also calls for Visa and MasterCard to lower the fees—for a certain period—that merchants pay to accept credit cards. The merchants valued the fee relief at $1.2 billion.