Yoon spoke at an event commemorating the country's historic March First independence movement against Japan's 1910-1945 occupation of Korea.
"Japan has transformed from a militaristic aggressor of the past into a partner that shares the same universal values with us," said Yoon, Reuters reported.
"Today Korea and Japan cooperate on issues of security and economy. We also work together to cope with global challenges... We must stand in solidarity with countries that share universal values."
Yoon's comments come after South Korea's presidential office said on Tuesday that officials from South Korea, the United States and Japan have held their first economic security dialogue, amid efforts to strengthen supply chain resilience and develop technology.
Though Japan and South Korea are at times uneasy neighbors, the three countries are keen to expand cooperation in various fields in the face of increased global tensions, a more assertive China and an unpredictable North Korea.
Last November, Yoon and Japanese Prime Minister Fumio Kishida agreed to continue discussions for a prompt resolution of pending issues, according to Yoon's office, as they seek to improve relations dogged by historical disputes.