The details of the settlement were not disclosed. The settlement filed Tuesday with the U.S. district court in Seattle ends the dispute between the e-commerce rivals.
"We are pleased that the matter has been settled," said Patty Smith, a spokeswoman for Amazon. A Barnes&Noble.com representative did not immediately return calls seeking comment.
Amazon sued Barnes&Noble.com in October 1999 charging that Barnes&Noble.com had essentially copied Amazon's 1-Click technology, which allows customers to skip several steps in the checkout process by presetting credit card and shipping information.
The suit set off a firestorm of protest on the Net, with many charging that the 1-Click technology was not innovative enough to warrant a patent. The suit also touched off a larger debate over Internet-related patents.
Amazon Chief Executive Officer Jeff Bezos responded to the criticism by calling for patent reform and by sponsoring an organization that investigated dubious patent claims.
Smith declined to say whether Barnes&Noble.com would be able to resume offering an expedited version its "Express Checkout" feature. Amazon won an injunction against use of the feature in December 1999.
Smith also declined to say whether Barnes&Noble.com paid to settle the suit, or whether it would license Amazon's technology.