The department said it lacked the legal authority to enact the rule, published in the closing days of Barack Obama's government. It was initially set to go into effect in March 2017.
But President Donald Trump's administration first froze it along with all other new regulations, then delayed it twice, and has now called it off altogether.
The USDA said today the rule would also have increased costs for producers and consumers.
It would also have expanded current requirements for livestock care and production methods.
More From This Section
The Organic Trade Association, the main group in the sector, condemned the decision.
It said the administration was irresponsibly ditching regulations that had been prepared carefully and were backed enthusiastically by organic producers and by consumers.
The OTA had already sued the administration for delaying implementation of the rule, and on Monday said it would push ahead with this lawsuit.