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.
The second landing was about the last chance for Hayabusa 2 because surface temperatures on Ryugu were increasing as the asteroid's orbit was bringing it closer to the sun.
Japan's space agency JAXA said Thursday that data transmitted from the spacecraft Hayabusa2 indicated its second successful touchdown on the distant asteroid Ryugu to complete a historic mission - to collect underground samples in hopes of finding clues to the origin of the solar system.
"We've collected a part of the solar system's history", project manager Yuichi Tsuda said at a jubilant press conference hours after the successful landing was confirmed.
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.
During the touchdown, Hayabusa2 would extend its sampling tube to the ground, shoot a pinball-size bullet to crack the surface and suck up the debris that got blasted off. Landing was a challenge for Hayabusa2 because of a risk of getting hit by dust and debris that remain at the crater, Kubota said.
Hayabusa2 is the first spacecraft to successfully collect underground samples from an asteroid.
The second touchdown required special preparations because any problems could mean the probe would lose the precious materials already gathered during its first landing. Based on the images returned from the spacecraft, the mission's manager Makoto Yoshikawa said: "It would be safe to say that extremely attractive materials are near the crater".
Scientists are hoping the probe will have collected unidentified materials believed to be "ejecta" from the blast after landing briefly in an area some 20 metres away from the centre of the crater.
"I'm really looking forward to analysing these materials", Yoshikawa said.
Hayabusa2 is expected to leave the asteroid to return to Earth at the end of next year, with the samples for scientific study.
Hayabusa2 observes the surface of Ryugu with its camera and sensing equipment but has also dispatched two tiny MINERVA-II rover robots as well as the French-German robot MASCOT to help surface observation.
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.
If the mission is a complete success, scientists will have these samples in front of them when Hayabusa2 returns to Earth in December 2020.
In April, a device called an impactor detached from the explorer and fired a copper plate weighing about 2 kilograms into the surface of Ryugu, successfully creating the crater, which is about 10 meters in diameter.