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.
In order to successfully find and gather the samples, an "impactor" was reportedly sent to the asteroid in order to create a crater for Hayabusa2 to probe.
"The landing was a huge success as (Hayabusa2) made a flawless move nearly in line with our expectations", said Takashi Kubota, a professor at JAXA's Institute of Space and Astronautical Science in Sagamihara, near Tokyo.
Japanese space probe Hayabusa2 on Thursday made its second successful landing on an asteroid located 244 million km from Earth, collecting underground samples that could provide information on the origin of the solar system.
Ryugu is now about 240 million kilometers from Earth.
If successful, it will be the second time it has landed on the desolate asteroid as part of a complex mission that has also involved sending rovers and robots.
Asteroids are small bodies that gradually formed when bits of cosmic dust repeatedly coalesced, and their makeup is believed to reflect conditions from the time the solar system was formed 4.6 billion years ago. "Project Manager Tsuda has declared that the 2nd touchdown was a success!", the agency said on its Twitter.
The second landing near that crater is meant to collect what JAXA hopes are the world's first underground samples from an asteroid.
"It would be safe to say that extremely attractive materials are near the crater", Tsuda said. Thursday's mission was to land inside that crater to collect scattered samples that scientists believe contain more valuable scientific data.
"I'm really looking forward to analyzing these materials", mission manager Makoto Yoshikawa said.
"The world is watching. We love you, take care Hayabusa2", the iconic musician told the team.
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.
Hayabusa2 is expected to leave the asteroid to return to Earth at the end of next year, with the samples set for scientific study.
Hayabusa2's photos of Ryugu, which means "Dragon Palace" in Japanese and refers to a castle at the bottom of the ocean in an ancient Japanese tale, show the asteroid has a rough surface full of boulders.
Some within JAXA had suggested aborting the second landing and having the probe return to Earth with the samples collected from the first landing.
It has already made history, including with the creation of the crater on Ryugu's surface.