Hayabusa2 is the first to successfully collect underground soil samples from an asteroid and comes ahead of a similar mission planned by the U.S. National Aeronautics and Space Administration (NASA) team at another asteroid.
In the final landing phase on Thursday, Hayabusa2 hovered at the height of 30 metres (100ft) above the asteroid and quickly found its landing marker left from the earlier mission.
More than 80 JAXA officials at the control room burst into applause at around 10:20 a.m., when data came in confirming a successful touchdown and the probe's subsequent ascent, with many making a V-sign for victory.
The brief landing Thursday is the second time Hayabusa2 has touched down on the desolate asteroid Ryugu, some 300 million kilometres (185 million miles) from Earth.
JAXA said the samples have been safely placed in a container, which will be moved to a capsule for secure storage. JAXA plans to send the spacecraft close to the asteroid again as early as next week to examine the landing site from above.More news: Arsenal captain Laurent Koscielny refuses to join pre-season tour
Japanese scientists have successfully landed an unmanned spacecraft on the distant asteroid Ryugu for the second time as part of an ongoing mission to help explore the origins of the solar system.
During the touchdown, the probe will collect the samples of material released from firing the projectile into the surface to later bring them to Earth.
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.More news: Recovered GoPro video shows final moments of Himalayas climbers
The complex multi-year Hayabusa2 mission has also involved sending rovers and robots down to the surface.
Scientists believe that the samples, which the Japanese probe will try to collect, may shed light on how the Solar System was created and how life appeared on Earth.
The Hayabusa2 mission has attracted worldwide attention, with Queen guitarist and astrophysicist Brian May sending a video to the probes team ahead of the landing. "We took a historic step", said Yuichi Tsuda, the Hayabusa2 project manager.
Ryugu, which means "Dragon Palace" in Japanese, refers to a castle at the bottom of the ocean in an ancient Japanese tale.
The original incarnation collected dust samples from a smaller asteroid, which is described as looking like a potato.More news: Ekta's Balaji Telefilms apologises on Kangana's behalf
Hayabusa-2 is expected to return to Earth with its samples in 2020.