Mr O'Brien claimed the meat and bonemeal incinerator, which would be the first of its kind in Ireland, would harm his business and would harm the health of local residents.
The company, National Byproducts, had opposed Mr O'Brien's application to challenge the decision.
Mr O'Brien had claimed the County Council had not been able to take into account the environmental effects of the development when making its decision, because Ireland had not properly implemented the European Commission's Environmental Impact Directive.
Mr Justice O'Caoimh granted the application and also imposed a stay on an appeal to An Bord Pleanála pending the outcome of the legal proceedings.
In a statement, Mr O'Brien said he and the owners of the nearby Coolmore Stud were very pleased with the decision.
He said the local community believed a meat and bonemeal incinerator would damage their health and livelihood.
Mr O'Brien's legal challenge to the incinerator is likely to go ahead later this year or early next year.
