The probe first landed on Ryugu in February and is believed to have collect samples of surface sand and rocks.
Its final descent to the asteroid from a height of 30 meters was made while the probe was on autonomous mode.
The Japan Aerospace Exploration Agency, or JAXA, said it has confirmed data showing Hayabusa2 touched down and rose safely. "Project Manager Tsuda has declared that the 2nd touchdown was a success!"
"Everything went perfectly, even better than flawless, as if Hayabusa were reading our minds", he said. JAXA plans to send the spacecraft close to the asteroid again as early as next week to examine the landing site from above.
Data indicates a spacecraft successfully landed on a distant asteroid and completed its historic mission of collecting underground samples that scientists hope will provide clues to the origin of the solar system, Japan's space agency said.More news: Korean calls for scrapping of tech export curbs
"Ryugu's surface has weathered due to the impact of solar winds, but the subsurface samples are believed to contain traces of the time when the solar system was created 4.6 billion years ago".
A webcast on the JAXA website showed that the probe began descending from an altitude of 20 kilometres (13 miles) on Wednesday, aiming to land near a crater that it created in April by firing a bullet into the asteroid's soil.
JAXA Research Director Takashi Kubota speaks to journalists during a press conference following the Hayabusa2 probe's touchdown on the asteroid Ryugu, at the Institute of Space and Astronautical Science (ISAS) of Japan Aerospace Exploration Agency (JAXA) in Sagamihara city, Kanagawa prefecture, July 11, 2019.
The second touchdown requires special preparations because any problems could mean the probe loses the precious materials already gathered during its first landing.
If successful, it will be the second time Hayabusa-2 has landed on the desolate asteroid as part of a complex mission that has also involved sending rovers and robots.More news: Man United very keen on signing 24-year-old
After the probe started its descent on Wednesday and collected the samples, "the probe's mission is nearly complete, and it will start its journey back to Earth at the end of this year", Kyodo said.
Ryugu, which means "Dragon Palace" in Japanese, refers to a castle at the bottom of the ocean in an ancient Japanese tale.
The touchdown is the last major part of Hayabusa2's mission, and when the probe returns to Earth next year scientists hope to learn more about the history of the solar system and even the origin of life from its samples.
"It would be safe to say that extremely attractive materials are near the crater", Hayabusa2 project manager Yuichi Tsuda said.
The Hayabusa2 mission has attracted global attention, with Queen guitarist and astrophysicist Brian May sending a video to the probe's team ahead of the landing. "We love you, take care Hayabusa2", the musician told the team.More news: Top 5 new insane Super Mario Maker 2 levels you can play
Hayabusa2 is expected to leave the asteroid to return to Earth at the end of next year, with the samples for scientific study.
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