The ovals' approach and merger was observed by several telescopes including one at the Pic-du-Midi Observatory in France, Nasa's Infrared Telescope Facility in Hawaii, and the Hubble Space Telescope.
For the first time, astronomers have seen two giant storms on Jupiter collide and merge to form an even bigger storm.
The two swirling wind systems are each about half the size of the Earth.
Researchers speculate that a similar merger of storms produced Jupiter's famous Great Red Spot, a hurricane that has persisted in the planet's atmosphere for more than 300 years.
The collision between the storms will help scientists understand more about the dynamics of Jupiter's turbulent atmosphere.
"Usually when we've seen two (storms) approaching each other, they bounce back away from each other," said Dr Glenn Orton of Nasa's Jet Propulsion Laboratory in California.
Swirling vortex
The current giant storm began forming about 60 years ago as three "white oval" storms in a band of Jupiter's atmosphere south of the Great Red Spot.
In the following decades until 1998, the storms sometimes approached each other but never collided.
But in early 1998, astronomers witnessed two of the ovals moving towards each other as Jupiter went out of sight from Earth, behind the Sun. When the planet came back into view, the two had become one.
"We weren't able to see how they came together that time," said Dr Orton.
Last year, however, the newly formed storm approached the third remaining oval. Winds within it were swirling counter-clockwise at about 470 km (290 miles) per hour. One was about 9,000 km (5,600 miles) across, the other slightly smaller.
A third, darker oval, this time swirling clockwise, formed temporarily between the two white ovals.
Joining forces
That type of intervening system would usually keep white ovals from colliding, the team proposed. But the middle storm appears to have been pushed even further south and torn apart, as all three passed near the Great Red Spot last December.
The disappearance of the opposite-swirling storm from between them cleared the way for the two white ovals to meet.
Their collision began in March and lasted about three weeks. The storms circled around each other counter-clockwise then merged into a single oval.
This single storm was about one third wider than either of the ovals had been beforehand.
The ovals' approach and merger was observed by several telescopes including one at the Pic-du-Midi Observatory in France, Nasa's Infrared Telescope Facility in Hawaii, and the Hubble Space Telescope.
Meanwhile, the Cassini spacecraft, approaching Jupiter for a fly-by in December, has taken a new image of the Great Red Spot.
As it passes by the giant planet, Cassini will make a series of measurements of Jupiter in several wavelengths of light as well as sampling energetic particles and magnetic fields.