South Australia is the first state in the country to cast a net over the pervasive piscine plastic, known as shoyu-tai.
Invented in Japan in the 1950s, they have become a popular way for diners to season their takeaway sushi.
But the fishy delights are too small to be captured by sorting machinery and often end up in landfills or as fugitive plastic, South Australia's Environment Minister Susan Close said.
"Single-use plastics are often used for seconds but they last a lifetime in our natural environment," she said.
"The small size of the fish-shaped soy containers means they're easily dropped, blown away, or washed into drains, making them a frequent component of beach and street litter."
South Australia is the first state in the country to ban the plastic soy fish, joining single-use cutlery, bags, coffee cups and takeaway containers on the list of prohibited items.
Manufacturer Asahi Sogyo makes a variety of other novelty soy-sauce containers -- originally known as lucky charms -- including small pigs and tiny bottles, according to the company's website.
The factory produces around a million "lucky charms" each day.
The South Australian government said restaurants will need to use alternative soy sauce carriers like sachets, squeezable packs, refillable or compostable containers.
Japanese restaurant owner Abby Zhang said the ban was a "positive step forward".
"We made a significant change a while back by switching from soy sauce fish containers to more sustainable alternatives, such as compostable sauce containers," Zhang said in a statement, adding customers were "incredibly supportive".
More than 400 million tonnes of plastic are produced globally each year, half of which is for single-use items.
While 15 percent of plastic waste is collected for recycling, only nine percent is actually recycled.
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