The meeting takes place in Panama and Latin American countries argued that declaring a sanctuary would help whale conservation and whale-watching.
The South Atlantic Ocean, spanning a vast area, extends from South America's East Coast to Africa's West Coast. The Buenos Aires Group, a coalition of 14 pro whale countries, had hoped to add the Ocean to two sanctuaries already approved by the IWC, the Indian Ocean Sanctuary and the Southern Whale Sanctuary.
A total of 33 nations supported the petition and 21 were against it, but 75% of the votes are needed for new petitions to take place. Observers noted that the vote was orderly and without rancour, in marked contrast with previous years which saw representatives walk out of the meeting to stop the meeting from being legal.
Marcos Pinta Gama, Brazil's commissioner to the IWC, said he was disappointed by the result, but pleased that the vote had happened.
"We believe that the sanctuary is a very important initiative in order to ensure the protection of whales within the whole South Atlantic, to promote the non-lethal use of cetaceans and and benign research that's important for conserving whales," he told BBC News.
Whale-watching and ecotourism, he said, were becoming important industries for coastal communities.
"In many countries including Brazil, those activities are bringing in financial resources to local communities, it's really expanding, and we think the sanctuary would very much strengthen this kind of activity in the region."
The legalities of Whaling today:
Objection: A country formally objects to the International Whaling Commission (IWC) moratorium, declaring itself exempt. Example: Norway and Iceland
Scientific: A nation issues unilateral "scientific permits"; any IWC member can do this. Example: Japan
Indigenous (aka Aboriginal subsistence): IWC grants permits to indigenous groups for subsistence food. Example: Greenland