Some 1,800 people were queuing in Tokyo to see the heat-proof pod, which had travelled in space with the unmanned craft for seven years, even before the exhibition opened in the morning, a Japan Aerospace Exploration Agency (JAXA) spokesman said.
The capsule, which journeyed billions of kilometres (miles), was fired back to Earth in June.
Technical problems had plagued the Hayabusa, which at one stage spun out of control and lost contact with JAXA for seven weeks, delaying the mission for three years until the asteroid and Earth re-aligned.
When it finally latched onto the potato-shaped Itokawa asteroid, a pellet-firing system designed to stir up dust malfunctioned, leaving it unclear how much material the probe was able to gather.
The space agency has said it found "minute particles" of what it hopes is asteroid dust in the capsule, but it is expected to take months to get the final results of the analysis.
The Hayabusa project has generated great excitement in Japan.
"I was so impressed that such a small thing came back to Japan after a seven-year space journey," said one of the visitors. "It is just amazing."