The highest level visit in five years was announced by the South's government only an hour before the delegation arrived at Incheon International Airport on Kim's personal presidential, Russian-made aircraft.
Pyongyang's 11-member delegation was led by Hwang Pyong So, 66, who - with five promotions this year alone - has become the second most powerful official after Kim. He is the top political officer for the Korean People's Army, the vice chairman of the powerful National Defense Commission and the vice marshal of the army.
The delegation also included Choe Ryong-hae, who had been the North’s second most powerful official until Hwang replaced him, and Kim Yang-gon, a top Communist Party official who had orchestrated numerous North-South high level talks in the past.
Details of the lunch meeting were not made public except that the two sides agreed to more talks at the end of this month or in November.
Hwang and his entourage attended the closing ceremony of the Asian Games later in the evening.
The visit comes amid rumors in Seoul about the health of Kim, who has made no public appearances since September 3 and recently skipped a high-profile event he usually attends. A recent official documentary showed footage from August of him limping, overweight and mentioned his "discomfort."
High-level North Korean visits to South Korea have been scarce since inter-Korean relations became strained after Park's conservative predecessor, Lee Myung-bak, took office in early 2008 with a tough line on the North. Attacks blamed on North Korea in 2010 killed 50 South Koreans.
Besides the North Korean test firings of about 100 rockets and missiles this year, both sides have leveled harsh criticism at each other, with North Korean state media calling the South Korean president a prostitute.
Word of the North's participation in the Asian Games was welcomed as a step forward.
North Korea boycotted the 1986 Asian Games and the 1988 Summer Olympics, both in Seoul, but attended the 2002 Asian Games in Busan, the 2003 University Games in Daegu and the 2005 Asian Athletics Championships in Incheon. Those last three came during an era of liberal governments in Seoul that were more accommodating to Pyongyang.
North Korea had said ahead of these games that it wanted to send both athletes and cheerleaders but later balked at sending cheerleaders because of what it called South Korean hostility.
The success at the Asian Games for both Koreas, which were in the top 10 for gold medals, is a source of pride for all Koreans, said one of the North Korean officials, Kim Yang Gon, a secretary in the ruling Workers' Party and senior official responsible for South Korean affairs, according to the YTN TV network. Choe Ryong Hae, another Workers' Party secretary and chairman of the State Physical Culture and Sports Guidance Commission, also attended.
The North Korean officials planned to fly back home later Saturday after the games' closing ceremonies.
The Associated Press contributed to this story.