The resumption of the so-called "2+2" talks involving senior foreign ministry and defence officials represented a slow thaw in practical diplomatic contacts despite a glacial rift in the overall relationship.
South Korean officials said the meeting, last held in 2009, covered regional security, defence policies and cooperation, but refused to disclose any further details.
The talks came at a particularly sensitive time as the region prepares to mark the 70th anniversary of the end of World War II, and with a rising tide of nationalism in Northeast Asia.
Bilateral ties have always been problematic given the bitter legacy of Japan's 1910-45 rule over the Korean peninsula.
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Seoul feels Tokyo has yet to fully atone for the excesses of its colonial rule and the forced recruitment of Korean women to wartime military brothels.
More recently, Tokyo has angered Seoul with renewed claims to a tiny set of South Korean-controlled islets, which have been the focus of a decades-old sovereignty row.
The foreign ministers of South Korea, China and Japan met in Seoul last month and pledged to work towards a trilateral leadership summit at "the earliest" opportunity, but observers say such a meet is unlikely in the short term.
But Park has refused to sit down one-on-one with Japanese Prime Minister Shinzo Abe, while Xi has only managed a brief meeting with Abe on the sidelines of an APEC gathering in Beijing last year.
The rift between Seoul and Tokyo is particularly disturbing for the United States, which wants its two key military allies in Asia to be united in the face of an increasingly assertive China.