They also showed it had, at the time, been unable to cause the bubonic form of plague or spread through fleas - abilities it evolved later.
The researchers, at the University of Copenhagen, say plague may have shaped early human populations.
Human history tells of three plague pandemics:
The Plague of Justinian began in AD541 and killed more than 25 million people
The Black Death started in China in 1334 and claimed the lives of up to half of Europeans
The Modern Plague, in China, emerged in the 1860s and led to 10 million deaths
There have also been suggestions of earlier plagues, such as the Plague of Athens in 430BC.
But now scientists have hurtled millennia back in time by studying 101 ancient skeletons.
The teeth of seven of them, from across western Europe and central Asia, contained evidence of Yersinia pestis infection - the killer bacterium that causes plague.
The oldest was 5,783 years old.
The analysis of those samples, published in the journal Cell, showed the bacterium was still lacking some of the killer traits that led it to cause death on a global scale.
In its early days, it could cause only septicaemic or pneumonic plague - which is nearly always deadly and would have been passed on by coughing.
By analysing the bacterium`s genetic code through history, the researchers estimate it took until 1000BC for plague to evolve into its more familiar form.
One mutation - acquiring the ymt gene - allowed the bacterium to survive inside the hostile environment of a flea`s gut.
It was one of the most signification mutations in the disease`s history, allowing it to spread rapidly.
Developing a separate gene, called pla, allowed the infection to penetrate different tissues and cause bubonic plague.
"It`s super-fascinating," lead researcher Prof Eske Willerslev said.
He told the BBC News website: "We show that plague was widespread 2,000 years earlier than normally thought.
"With time, these studies will help us to understand how diseases are formed, how they originate and develop."
Prof Willerslev believes the plague could have had a huge impact on early human populations.
Previous studies have shown that rather than growing gradually, populations in Europe may have declined by up to 60% at some points in their history, with plague a potential culprit.
It was also a time of huge migration in the region.
"You see these very abrupt population replacements, people moved into northern Europe from central Asia, replacing the existing populations - kinds of very abrupt migrations [that] fit very well with plague playing a major role," Prof Willerslev said.
Plague remains endemic in some countries. In 2013, there were 783 cases reported worldwide, including 126 deaths.
While most cases are in Africa, even the US continues to have cases of plague.
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