The Federal Court class action, led by Brett Cattle Company, claimed the ban cost cattle producers hundreds of millions of dollars.
The issue of live exports had been controversial for many years but became volcanic when an ABC Four Corners program in May, 2011, aired footage showing the poor treatment of animals in facilities in Indonesia.
The judge said the minister made the ban order "shutting his eyes to the risk that it might be invalid and to the damage that it was calculated to cause persons in the position of Brett Cattle".
He was satisfied the minister was recklessly indifferent regarding his ability to make such an order without power of exception, and to the injury it would produce.
“Such a total prohibition was capricious and unreasonable and made the ban order invalid,” the judge said.
“I have found that, had the minister acted lawfully, he would have made a control order on about June 9 or 10, 2011, that contained an exceptions power and that Elders and Santori would have been able to obtain approvals to export to Indonesia under it without delay.”
He ordered the minister and the Commonwealth pay the legal costs of the proceedings, noting Brett Cattle was entitled to substantial damages.
The parties would need to return to court at a later date in order to determine compensation for the class action members.