Prime Minister Shinzo Abe attended a ceremony at the South Korean embassy in Tokyo, while President Park Geun-hey did the same and attended the Japanese embassy in Seoul.
Both leaders made polite statements about the state of bilateral relations and avoided references to the controversies that have distanced the nations.
Attending the ceremonies was not initially included in Abe and Park's agendas but the governments announced the decision on Sunday night.
The decision is in tune with Washington's desire to see reconciliation between its main allies in Asia.
The relation between Japan and South Korea has reached its lowest point since World War Two.
According to a survey by influential Japanese journal Yomiuri, 73 percent of the Japanese does not trust its neighbors, while 85 percent of South Koreans think alike.