The decision by Seoul's Foreign Ministry follows a summit between South Korean President Yoon Suk Yeol and his Japanese counterpart Fumio Kishida in Tokyo last week.
During the first top-level bilateral meeting in 12 years, the two sides agreed to mend fences over historical disputes stemming from Japan's 35-year colonial rule of the Korean peninsula.
Yoon also reportedly told Kishida he wanted a "complete normalisation" of a 2016 military agreement called the General Security of Military Information Agreement (GSOMIA).
The agreement aims to allow the two US allies to share military secrets, particularly over North Korea's nuclear and missile capacity, but Seoul threatened to tear it up in 2019 as relations with Tokyo soured.
Seoul "notified Japan via a written document" of its decision to normalise the military pact, its foreign ministry said in a statement Tuesday, in a move that had been reported over the weekend.
This has "laid the groundwork for strengthened military intelligence sharing between South Korea-Japan and among South Korea-Japan-the United States by removing uncertainties", it added.
Yoon is seeking to boost ties with Tokyo, citing security challenges on the peninsula, despite strong domestic opposition, including from victims of Japanese forced labour.
He dismissed criticism as "political" Tuesday, telling a cabinet meeting that Tokyo has "expressed remorse and apology for historical issues on dozens of occasions".
Seoul's 2019 threat to scrap the GSOMIA came as relations with Tokyo hit a new low over trade disputes and the row over forced labour.
After opposition from America, South Korea kept the deal in place, but experts say its practical application was thought to have been limited by strained relations between the two countries.
Confronted with Pyongyang's growing aggression and flurry of missile tests, the neighbours have increasingly sought to bury the hatchet.
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