Japanese Prime Minister Suga Yoshihide and President Joko Widodo have called for continued cooperation on matters including health, security and the economy.
After the summit meeting, the leaders held a news conference.
Suga said, "I told President Joko that ASEAN is a key player in ensuring a free and open Indo-Pacific. I stressed Japan's commitment to leading efforts to contribute to peace and stability in this region."
The leaders agreed to work closely to address various regional issues, such as China's increasing maritime activities.
They committed to stepping up cooperation in the field of security, including a meeting of their foreign and defense ministers.
They also plan to speed up negotiations on the transfer of defense equipment to Indonesia.
Suga offered about 470 million dollars in loans to Indonesia to help limit the economic fallout from the coronavirus pandemic.
The leaders also agreed to gradually relax travel restrictions between their countries -- especially for business people, as well as nurses and caregivers coming to work in Japan.
The Indonesian president touted the need for strength in numbers amid an increasingly uncertain global situation.
Indonesian President Joko Widodo said, "The partnership between Indonesia and Japan should strengthen multilateral cooperation. I stressed the importance of strengthening this cooperation amid sharpened competition among world powers. The spirit of inclusive cooperation needs to increase in the Indo-Pacific region. I hope that the South China Sea will be peaceful and stable."
Suga is on his first overseas trip since taking office last month. He was in Vietnam before Indonesia.