At that time, yeast just fell into the fermenting vats from the air and microbiology did its thing with the help of some human brawn and brains.
As fermentation technology advanced, people realized that they could isolate the yeast strains which hung around the breweries waiting for a pot of rice, water and koji to get cozy with.
Researchers isolated the first strain of sake yeast in 1898. They continued to discover new strains from then on and soon yeast were bottled in liquid form and distributed by The Brewing Society of Japan, 日本醸造協会.
This made the process of brewing a much more consistent and controlled practice, leading to most brewers abandoning the traditional way of working with the ambient yeasts that hung in the rafters of their brewery.