Hayabusa 2 will depart Ryugu in December 2019 and return to Earth by the end of 2020 with its precious cargo of samples to be analyzed by scientists.
The Hayabusa2 mission has attracted global attention, with Queen guitarist and astrophysicist Brian May sending a video to the probes team ahead of the landing.
According to JAXA, the underground materials have not been affected by space radiation and other factors, which could provide additional information to earlier samples taken from the surface.
The actual landing was just a few seconds.
The initial touchdown on the asteroid was postponed from October previous year, as JAXA found the surface of the asteroid, which at the time was about 300 million km from Earth and 900 meters in diameter, to be rockier than it first thought and needed more time to ensure the safe landing of the probe.
"It would be safe to say that extremely attractive materials are near the crater", Tsuda said.
Project manager Yuichi Tsuda stated from the mission control room that the touchdown was a success, and that the event "marked a new chapter in history".
The manoeuvre that brought the Hayabusa-2 into contact with the surface of asteroid Ryugu this morning was greeted with relief and renewed confidence by the control room of the Japanese Space Agency (JAXA) in Sagamihara, in the eastern prefecture of Kanagawa (picture 2).
When the two objects finally met, the Hayabusa2 deployed two miniature rovers to the asteroid's surface, which have been conducting research on the origins of the solar system across the asteroids surface ever since.
At about the size of a large refrigerator and equipped with solar panels to keep it powered, Hayabusa2 is the successor to JAXA's first asteroid explorer, Hayabusa - Japanese for falcon.
Some within JAXA had suggested aborting the second landing and having the probe return to Earth with the samples collected from the first landing.
Ryugu has a diameter of about 900 meters and is believed to contain more carbon than the Itokawa asteroid, leaving open the possibility that Ryugu holds organic substances. Hence, scientists hope to get more data on the origins of the Solar System.
Hayabusa2 reached its stationary position above Ryugu in June a year ago after traveling 3.2 billion km.
John Bridges, a professor of planetary science at the UK's University of Leicester, told CNN that the Hayabusa 2 mission is interesting because of Ryugu's C-class status.
That probe returned with dust samples from a smaller, potato-shaped asteroid in 2010, despite various setbacks during its epic seven-year odyssey and was hailed as a scientific triumph.