The strategy change is part of an agreement that the music retailer's parent company Bertelsmann and CDNow plan to unveil in the coming weeks.
A Bertelsmann representative declined to elaborate on the terms of the deal, but maintained that the German media giant has not sold the retail site to Amazon.
"CDNow remains a part of BeMusic," Bertelsmann spokeswoman Melinda Meals said. BeMusic, a division of Bertelsmann, sells music directly to consumers.
Many online retailers have used affiliate programs as marketing tools. An affiliate hosts a retailer's link on its Web page. That retailer pays the affiliate a certain fee every time a surfer clicks on the link or buys merchandise from the linked site.
Affiliates will have until Dec. 3 to remove links and all references to CDNow.
Meals declined to comment on a report in music industry magazine Billboard speculating that Amazon would take over some of the back-end operations in running CDNow.
An Amazon representative confirmed that the company had reached an agreement with CDNow, but she declined to offer additional details.