Foreign Minister Seiji Maehara and South Korean ambassador to Japan Kwon Chul-Hyun signed the agreement in Tokyo, the ministry said in a statement.
"Japan and South Korea are good partners to promote peaceful use of nuclear power while ensuring nuclear non-proliferation, nuclear energy safety and security," Maehara told the ambassador, quoted in the statement.
Japan and South Korea have been rivals in international biddings for nuclear power plants in emerging nations.
In October Japan secured a contract for building two nuclear reactors in Vietnam while South Korea won a deal in December to build four reactors in the United Arab Emirates.
But under the pact, which will take effect after parliaments of both countries endorse it, mainly Japanese firms with a longer history of developing nuclear power plants are expected to start exporting technologies and equipment to South Korea.
Japan, which was eclipsed this year by China as Asia's biggest economy and has a shrinking population because of its low birth rate, is searching for new markets to export infrastructure technologies, including power plants.
Japan has concluded a bilateral nuclear energy pact with six countries and the European Union while South Korea has a similar deal with 14 states, the Japanese foreign ministry said.