The successful contact with the Ryugu asteroid was met with relief and cheering in the control room at Japan's space agency, JAXA.
Hayabusa2 is the first to successfully collect underground soil samples from an asteroid and comes ahead of a similar mission planned by the US National Aeronautics and Space Administration team at another asteroid.
As if landing on large planets weren't hard enough, the space scientists and engineers in at JAXA (Japan Aerospace Exploration Agency) wanted to land a spacecraft on an asteroid.
This is one of the most important missions of the spacecraft, which is scheduled to return to Earth next year with the samples gathered from the Ryugu asteroid, which is around 900 metres in diameter with a slightly cubical shape and is considered among the oldest bodies in the solar system, reports Efe news.
Hayabusa2 is equipped with various types of technology to help it observe and sample Ryugu, including a camera, that has beamed back images of the desolate asteroid's surface, and sensing equipment to record an array of data.
A Japanese spacecraft has touched down on a faraway asteroid, where it will collect space rock that may hold clues to how the Solar System evolved.
The probe first reached the Ryugu asteroid in June 2018, carrying out observations and measurements for months.
Back in April, the probe fired an "impactor" at the surface of the space rock Ryugu, which is 185 million miles (300 million kilometres) from earth, to create a crater.
This is huge because it's the very first time something from an inside of an asteroid has been collected.
The photos are also a mythical reference, as Ryugu translates to "Dragon Palace" in Japanese and refers to a castle at the bottom of the ocean in an ancient Japanese tale.
Among the Hayabusa2 mission's innovations are its ability to create a crater on the surface of the asteroid, and its transport of the MASCOT robot.
But its mission has already made history, including with the creation of the crater on Ryugu's surface.
Thursday's touchdown was planned to gather flawless materials from underneath the outside of the space rock that could give experiences into what the close planetary system resembled at its introduction to the world, some 4.6 billion years back. In the final landing phase Thursday, Hayabusa2 hovered at the height of 30 meters (100 feet) above the asteroid and quickly found its landing marker left from the earlier mission.
Research director Takashi Kubta told reporters that the touchdown operation was "more than perfect", adding that project manager Yuichi Tsuda told the team: "We have made history".
A second touchdown and collection of subsurface samples was considered risky as any problems that happen now could result in the loss of precious surface samples which the probe had collected previously. Hayabusa2, for its second sample, would then capture the debris as it floated up.