Superior Court Judge Michael Stern said a jury should decide the numerous factual disputes about whether the hit-making producer is owed any money.
Jones sued the estate and Sony Music Entertainment in 2013, seeking at least $10 million.
He contends the defendants re-edited songs for the This Is It film and a pair of Cirque du Soleil shows to deprive him of royalties and production fees.
Jones is also seeking a credit on the film that was done by using Jackson’s final rehearsals for a planned series of comeback concerts in London.
The producer worked with Jackson on three of his most popular solo albums: Off the Wall, Thriller and Bad.
Jackson’s estate and Sony Music have denied wrongdoing and sought dismissal of the case.
The popularity of Jackson’s music soared after his death in 2009.
Jackson’s hits “Billie Jean,” ”Thriller” and “Don’t Stop ‘Til You Get Enough” are among the songs Jones claims were re-edited to deprive him of royalties and a producer’s fee.
The lawsuit states his contracts call for him to have the first opportunity to re-edit or alter the songs, in part to protect his reputation.