This is only the second time such an impact has been observed. The first was almost exactly 15 years ago, when more than 20 fragments of comet Shoemaker-Levy 9 collided with the gas giant.
"This has all the hallmarks of an impact event, very similar to Shoemaker-Levy 9," said Leigh Fletcher, an astronomer at NASA's Jet Propulsion Lab in Pasadena, California. "We're all extremely excited."
The impact was discovered by amateur astronomer Anthony Wesley in Murrumbateman, Australia at about 1330 GMT on Sunday. Wesley noticed a black spot in Jupiter's south polar region - but he very nearly stopped observing before he saw it.
"By 1am I was ready to quit ... then changed my mind and decided to carry on for another half hour or so," he wrote in his observation report. Initially he suspected he was seeing one of Jupiter's moons or a moon's shadow on the planet, but the location, size and speed of the spot ruled out that possibility.
'Stroke of luck'
After checking images taken two nights earlier and not seeing the spot, he realised he had found something new and began emailing others.
Among the people he contacted were Fletcher and Glenn Orton, also at JPL. They had serendipitously scheduled observing time on NASA's InfraRed Telescope Facility in Hawaii for that night.
"It was a fantastic stroke of luck," Orton told New Scientist.
Their team began observations at about 1000 GMT on 20 July, and after six hours of observing confirmed that the spot was an impact and not a weather event.
"It's completely unlike any of the weather phenomena that we observe on Jupiter," Orton says.
The first clue was a near-infrared image of the upper atmosphere above the impact site. An impact would make a splash like a stone thrown into a pool, scattering material in the atmosphere upwards. This material would then reflect sunlight, appearing as a bright spot at near-infrared wavelengths.
And that's exactly what the team saw. "Our first image showed a really bright object right where that black scar was, and immediately we knew this was an impact," Orton says. "There's no natural phenomenon that creates a black spot and bright particles like that."
Supporting evidence came from measurements of Jupiter's temperature. Thermal images also showed a bright spot where the impact took place, meaning the impact warmed up the lower atmosphere in that area.
The researchers have also found hints of higher-than-normal amounts of ammonia in the upper atmosphere. Extra ammonia had been churned up by the previous Shoemaker-Levy comet impact.
The Shoemaker-Levy impact also introduced some exotic chemistry into Jupiter's atmosphere. The energy from the collision fused some of the original atmospheric components into new molecules, such as hydrogen cyanide.
Scientists hope this new impact has done the same thing, since that would allow them to follow the new materials and learn how the atmosphere moves with time.
So what was the impactor? "Not a clue," Orton says. He speculates that it could have been a block of ice from somewhere in Jupiter's neighborhood, or a wandering comet that was too faint for astronomers to detect before the impact.
Without having seen it, scientists can't tell how large the object was. "But the impact scar we're seeing is about the same size as one of Jupiter's big storms, Oval BA, Fletcher told New Scientist. "That, I believe, is about the size of the Earth."