The yeast conferred characteristics that for the first time meant that beer could ferment in the cold.
Writing in the journal Proceedings of the National Academy of Sciences, an international team of researchers describes how they discovered the organism after an exhaustive search.
Dubbed Saccharomyces eubayanus, the yeast was traced to Patagonian beech forests at the tip of South America.
It lives on sugar within beech galls, causing spontaneous fermentation that generates alcohol.
Analysis showed it was unlike any other known species of wild yeast, but 99.5 per cent similar to the unidentified half of the lager hybrid.
"People have been hunting for this thing for decades," said Professor Chris Hittinger, from the University of Wisconsin-Madison in the US.
"And now we've found it. It is clearly the missing species."
The yeast may have been transported to Europe on a piece of wood or in the stomach of a fruit fly, the researchers believe.
Genetic mutations accelerated by the brewing process refined the lager yeast's ability to produce cold beer.
"Our discovery suggests that hybridisation instantaneously formed an imperfect 'proto-lager' yeast that was more cold-tolerant than ale yeast and ideal for the cool Bavarian lagering process," said Professor Hittinger.
"After adding some new variation for brewers to exploit, its sugar metabolism probably became more like ale yeast and better at producing beer."
- AAP