Visitors laid white flowers at the sombre stone structure in Rangoon, in tribute to the 17 South Koreans killed during the attack at the Martyrs' Mausoleum.
South Korean Foreign Minister Yun Byung-Se hailed the event as "a landmark in our relations", adding that Seoul would pursue a "much stronger friendship" with the people of Myanmar.
The bombing targeted then South Korean president Chun Doo-Hwan, who had been due to lay a wreath to commemorate Myanmar's independence hero Aung San, the father of pro-democracy leader Aung San Suu Kyi.
Chun's life was spared thanks to traffic congestion. He was only minutes away from the mausoleum when the bomb, concealed in the structure's roof, went off just above the gathered presidential entourage.
Among the dead were South Korea's then foreign minister Lee Beom-Seok, as well as the deputy prime minister and industry minister. Four Myanmar nationals were also killed in the blast.
Myanmar police later identified three North Korean agents who had travelled by ship to Rangoon and received explosives in the North Korean embassy.
Two of them were arrested, while a third managed to kill three soldiers before being cornered and shot dead.
Myanmar broke off diplomatic ties with the North as a result of the attack, but the ruling generals restored ties in 2007.
Myanmar has since emerged from military rule with a reformist quasi-civilian government taking power in 2011.
The following year the United States praised the government for pledging to abide by a UN Security Council resolution prohibiting the procurement of military goods and assistance from North Korea.
But last December the US Treasury levelled sanctions against a Myanmar military official and three Myanmar businesses for trading arms with Pyongyang.
A Myanmar official, who asked not to be named, said the North's nuclear programme had been discussed in meetings between Yun and his Myanmar counterpart.
"Myanmar is very principled in opposing the North Korean's nuclear weapons programmes," Yun told AFP.