Four snapper breeding areas of northern Spencer Gulf and one in Saint Vincent Gulf will be closed from December 15 until the end of January.
Bigger areas had been proposed but were reduced after public consultation.
Association president Michael Fooks said a balance would be achieved which would help ensure sustainability of the fishery.
"It maintains access to some of the fishery for the markets," he said.
"It means that people have an income and that they know the snapper stocks will be protected for the long-term.
"The guys on the ground ... believe it's very important and, even though it will affect their business in some way, they're prepared to wear that for the benefit of the snapper fishery."