Kim marked the anniversary at Kumsusan Palace of the Sun, where the embalmed bodies of his father and North Korea founder Kim Il Sung have been placed.
Pyongyang's state-controlled news agency KCNA reported "Comrade Kim" paid tribute to his father at exactly midnight.
Top North Korean officials including Choe Ryong Hae, vice chairman of the central committee of the Workers' Party, along with former Foreign Minister Ri Su Yong and others accompanied Kim to the site, according to South Korean news agency Yonhap.
"All participants agreed to make a firm commitment to realize the patriotic desires of General Kim Jong Il by completing the historical cause of strengthening the party and the construction of a strong socialist power," KCNA stated.
The event comes after North Korea released pre-recorded footage showing a separate event marking the birth anniversary, South Korean newspaper Kyunghyang Shinmun reported.
The video released late Thursday shows Hwang Pyong So, previously believed to have been purged, appearing at the public event along with other Workers' Party officials.
The official is making an appearance about two weeks after Seoul's spy agency said Hwang, one of the most powerful people in Pyongyang, had been removed from his position and was receiving "ideological reeducation" at a state school.
North Korea has outwardly changed its approach to the South following reconciliation that is ongoing during the 2018 Pyeongchang Winter Olympics.