U.S. District Judge Phyllis Hamilton in Oakland, California, on Tuesday ordered that the case be dismissed at the companies' request.
The dismissal came after Apple issued to Amazon a covenant not to sue, eliminating the need for Amazon to pursue a related counterclaim.
Apple originally filed the suit back in March 2011. At the time, Apple asked for a court order to prevent the company from using the "App Store" name, as well as for unspecified damages. Apple claimed that it would "confuse and mislead customers" if Amazon used the name as well.
Earlier this year Amazon won a dismissal of a portion of the lawsuit as well.