President Moon Jae-in sent a congratulatory letter to Japan's Prime Minister.
Fumio Kishida was re-elected after his ruling party won a majority in parliamentary elections last month.
Seoul's government hopes for efforts from both sides to pool wisdom to deal with pending global issues, such as COVID-19 and climate change.
Bilateral ties have been on edge over historical issues, including wartime sex slavery and forced labor.
Last month, the two leaders spoke on the phone for the first time and agreed to make efforts to speed up diplomatic consultations on the historical dispute.