Ulysses has long been seen as a classic novel
The Reader's Edition of Ulysses, published in the UK by Macmillan, included spelling and punctuation corrections, and some unpublished material.
But the Joyce estate said the new material, taken from archive manuscripts, was protected by copyright and should not have been published.
On Thursday Mr Justice Lloyd ruled in favour of the estate - and ordered that 1,000 undistributed copies of the work be handed over to the Joyce estate.
But the judge suspended the order pending an appeal by the publishers, and said that this would allow them to dispose of their existing stock in the meantime.
The novel, which was prosecuted for obscenity when it was originally issued in serial form in 1918, was eventually published in Paris in 1922.
A British edition did not follow until 1937.
The book uses a "stream of consciousness" method to describe one day in the Dublin lives of three characters, Leopold Bloom, his wife Molly and Stephen Dedalus.
It is regarded as one of the great literary works of the 20th Century.
Scholarship
The Reader's Edition was edited by Dublin-based Danis Rose and published by Picador under the Macmillan imprint in 1997.
It incorporated the results of Joycean scholarship and research.
The judge held that almost all of the new text had previously been published over the years during Joyce's lifetime and therefore did not infringe copyright.
But some 250 of the words were taken from manuscripts not published until the establishment of the James Joyce Archive in 1970s - which were still protected by copyright held by the author's estate.
The judge rejected another claim by the Joyce estate, that Macmillan and Mr Rose had been guilty of "passing off" the Reader's Edition of Ulysses as something which it was not.