The spot was first seen by an amateur Australian astronomer Anthony Wesley An object that hit Jupiter last year with a force equivalent to a few thousand nuclear bombs, which left it with a scar the size of Pacific Ocean was probably an asteroid, say astronomers.
Images of the "bruise" captured by the Hubble telescope show the aftermath of an asteroid striking a planet.
It could provide clues about what might happen if a similar object hit Earth.
The spot was first seen in 2009 by an Australian amateur astronomer.
The astronomer in question, Anthony Wesley, has recently taken another striking image of an bright fireball hitting the gas giant. Scientists believe it to be a meteoroid - a small particle of space debris.
A team of scientists described in the Astrophysical Journal Letters how they compared the 2009 Hubble images with those of scars left on Jupiter by a comet in 1994.
Jupiter impacts were thought to be quite rare. After the latest collision with a comet called P/Shoemaker-Levy 9, or SL9, astronomers didn't expect any other strikes for at least several hundred years.
That is why some 500m-wide space rock plunging into the gas giant's atmosphere was rather unexpected, said astronomer Heidi Hammel of the Space Science Institute in Boulder, Colorado, who led the study.
"This solitary event caught us by surprise," she said.
"We can only see the aftermath of the impact, but fortunately we do have the 1994 Hubble observations that captured the full range of impact phenomena, including the nature of the objects from pre-impact observations."
Dr Hammel's team used the Hubble telescope's Wide Field Camera 3 to zoom in on the blemish near the Jupiter's southern pole and captured several sharp ultraviolet images.
Astronomers spotted a flash on Jupiter - possibly a meteoroid striking the planet The scientists compared the pictures with those of the scars left by SL9 15 years earlier and saw important differences between the two impacts.
Most importantly, they found no "halo" around the latest collision site. A comet would have generated a halo of fine dust as it impacted the surface.
The clues helped them to conclude that the mystery object was probably not a dusty comet but a solid space rock that perhaps came from a nearby asteroid belt.
Agustin Sanchez-Lavega of the University of the Basque Country in Bilbao, Spain called Jupiter a "natural laboratory" to see what might happen to our planet in the event of a similar collision.
"It would be a catastrophe," he said.
"The Jupiter impact produced a pattern of debris some 5,000km long and 2,800 km wide - half the size of the Earth. And even if the response of the Earth atmosphere is different from that of Jupiter, entire continents could be destroyed."
The scientist also commented on the latest flash spotted on Jupiter by Anthony Wesley and another amateur, Christopher Go from the Philippines.
It is believed to be the very first image of a meteoroid hitting a planet.
This also shows that amateur astronomers now have the necessary high quality technology to capture such events that only last a few seconds.
"We cannot devote the Hubble space telescope or other telescopes to observe Jupiter regularly, it is impossible," he said.
"And the amateurs make a very good survey of what is happening there, contributing to our database."