Howard Mann, who used michaeljacksonsecretvault.com, MJgives.com and similar domain names to sell Jackson's music and other memorabilia, was also barred from using the "Thriller" singer's image without the permission of his estate.
The two sides announced the settlement in Los Angeles federal court hours before a trial was due to start to determine how much Mann owes the estate.
He was found liable for infringing the dead singer's intellectual property in a court ruling in August. The websites were also ordered shut down.
The estate holds the copyright to Jackson's image and music for the benefit of the singer's mother Katherine and his three children.
Howard Weitzman and Zia Modabber, the attorney's for Jackson's estate, said in a statement that the "settlement seems appropriate for all concerned".
Mann's attorneys could not be reached for comment.
The executors of Jackson's estate filed the case against Mann in January 2011, 18 months after the "Thriller" singer's sudden death in Los Angeles from an overdose of the surgical anesthetic propofol.
Mann worked with Katherine Jackson on several projects, including a 2010 "Never Can Say Goodbye" coffee table book featuring recollections of her son, and a DVD and calendar featuring what were described as never before seen photos and videos.
All were sold through the "secretvault" website. Mann claimed he obtained the rights to the material at a bankruptcy sale involving members of Jackson's family several years ago.
He also used copyright-protected clips of Jackson's song "Destiny", a logo featuring the self-styled "King of Pop" and art from the posthumous concert movie "This Is It" on his websites.
(Reporting By Jill Serjeant; Editing by David Gregorio)
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