The accord was signed at the Asia-Pacific Economic Cooperation summit that concluded in Yokohama Sunday.
The treaty, which must be approved by Japan's parliament, calls specifically for the return of 1,205 books from Korea's Joseon Dynasty, which lasted from 1392 until 1910.
South Korea's Yonhap news service said the two nations saw the accord as a significant step in tightening their relationship.
The Seoul government estimates that 60,000 cultural artifacts were shipped to Japan during the colonial period. More than 1,400 were returned when Japan formally recognized independent South Korea in 1965.