The District Court in Seattle officially ended the court case on Tuesday, though details of the settlement were not disclosed.
Amazon.com representatives in Europe were unable to comment on the case, and Barnesandnoble.com could not immediately be reached for comment.
One time Amazon.com's one-click system allows repeat online customers to place orders without re-entering credit card or address information. Included in the patent is the technology that stores billing and shipping data.
Amazon.com, which started offering its one-click feature in September 1997 and received a patent for it in September 1999, sued Barnesandnoble.com in October 1999 for patent infringement.
In December 1999, Amazon obtained a preliminary court injunction against Barnesandnoble.com that prevented its competitor from using the one-click system, but the injunction was overruled in February of last year.
Patent critics Amazon.com, its CEO Jeff Bezos and the US Patent and Trade Office (PTO) have been criticized by independent software developers for obtaining and granting software patents.
The online retailer was using the patent to undercut its competition, and the PTO showed a clear lack of understanding of software prior art in granting the patent claim, the critics said.
Amazon also licenses the technology to Apple, who uses it on its Apple Store.