A federal judge in New York ruled in favor of Rowling in September, permanently blocking publication of the reference guide.
He also awarded Rowling and Warner Bros. Entertainment Inc. $6,750 in statutory damages.
Vander Ark, a former school librarian, and his publisher say the revised version meets specifications for such a book laid out in the judge's ruling.
During the trial, the small publisher did not contest that the lexicon infringes on Rowling's copyright, but argued it was a fair use allowable by law for reference books. The judge ruled Vander Ark went too far.
Though Rowling had once praised Vander Ark's Web site, she testified earlier this year that the lexicon was nothing more than a rearrangement of the material.
Rowling's "The Tales of Beedle the Bard" became available Thursday. It's a collection of five fables mentioned in her saga about the boy wizard.