Visiting the city a day after his first summit with Russian President Vladimir Putin, Kim had been scheduled to take part in the ceremony at 10:00 am (0000 GMT) but at first was a no-show.
As soldiers and a military band waited in the rain, word came that the event - at a World War II memorial to Russia's Pacific Fleet - had been cancelled and the red carpet was rolled up.
Around noon the honour guard returned and a few minutes later Kim pulled up in his black limousine. The band played solemn music and ceremonial guards placed a large wreath on a stand next to an eternal flame.
In a black hat and double-breasted overcoat, Kim went up to the wreath briefly, then stepped back and stood with his hat in his hand, looking sombre. Behind him stood local officials holding carnations, including regional governor Oleg Kozhemyako.
All aboard for Vladivostok: Kim follows in father's tracks
A ceremonial guard marched past, Kim spoke briefly with a Russian military official, then got back into his limousine and drove off with a motorcade.
Kim arrived on Wednesday in the Pacific coast port on his armoured train, then met with Putin for five hours on Thursday for a summit that saw the two leaders vow to pursue closer ties.
Putin left the same day for China and Kim stayed on for a series of cultural events.
Russian media had reported that he was due to visit Vladivostok's aquarium and see a ballet, but on Friday said his programme had been significantly reduced and that Kim would be departing earlier than planned.
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