Judge Robert Patterson said in a ruling Monday that Rowling had proven that Steven Vander Ark's "Harry Potter Lexicon" would cause her irreparable harm as a writer.
The British author sued Michigan-based RDR Books last year to stop publication of the book claiming copyright infringement.
Rowling claimed the book is nothing more than a rearrangement of her own material and told the judge it copied so much of her work that it amounted to plagiarism.
"I think it's atrocious. I think it's sloppy. I think there's very little research," she testified last April. "This book constitutes wholesale theft of 17 years of my hard work."
RDR's lawyer, Anthony Falzone, had defended the lexicon as a reference guide, calling it a legitimate effort "to organize and discuss the complicated and very elaborate world of Harry Potter."
The small publisher did not contest that the lexicon infringed upon Rowling's copyright, but argued that it is a fair use allowable by law for reference books.
Rowling's Potter series has been published in 64 languages, sold more than 400 million copies and produced a film franchise that has pulled in $4.5 billion at the worldwide box office.
Vander Ark, 50, runs the popular Harry Potter Lexicon Web site.
He said he joined an adult online discussion group devoted to the "Harry Potter" books in 1999 before launching his own site as a hobby a year later. The Web site attracts about 1.5 million page views per month and contributions from people all over the world.
After Rowling released the final chapter in the "Harry Potter" series, Vander Ark was contacted by an RDR Books employee, who told him that publication of the lexicon would not violate copyright law, he said.
He said it was decided that the lexicon would include sections from the Lexicon Web site that give descriptions and commentary on individual names, places, spells and creatures from Harry Potter stories.
Still, to protect himself, Vander Ark said he insisted that RDR Books include a clause in his contract that the publisher would defend and pay any damages that might result from claims against him.