The discovery shows that black holes with powerful jets may be more common than previously thought in the first few billion years after the Big Bang.
The light detected from this jet was emitted when the universe was only 2.7 billion years old, a fifth of its present age.
At this point, the intensity of the cosmic microwave background radiation (CMB) left over from the Big Bang was much greater than it is today.
"We essentially stumbled onto this remarkable jet because it happened to be in Chandra's field of view while we were observing something else," explained co-author Lukasz Stawarz of Jagiellonian University in Poland.
The length of the jet, found in the system known as B3 0727+409, is at least 300,000 light years.
Many long jets emitted by supermassive black holes have been detected in the nearby universe, but exactly how these jets give off X-rays has remained a matter of debate.
In B3 0727+409, it appears that the CMB is being boosted to X-ray wavelengths.
"Because we are seeing this jet when the universe was less than three billion years old, the jet is about 150 times brighter in X-rays than it would be in the nearby Universe," said Aurora Simionescu at Jaxa's Institute of Space and Astronautical Studies (ISAS) who led the study.
Electrons in black hole jets usually emit strongly at radio wavelengths, so typically these systems are found using radio observations.
The discovery of the jet in B3 0727+409 is special because so far almost no radio signal has been detected from this object, while it is easily seen in the X-ray image.
"Supermassive black hole activity, including the launching of jets, may be different in the early Universe than what we see later on," noted study co-author Teddy Cheung of the Naval Research Laboratory in Washington, D.C.
By studying more of these distant jets, scientist can start to grasp how the properties of supermassive black holes might change over billions of years.
The results were published in The Astrophysical Journal Letters.