They did so gradually – starting in 1945. Although the repercussions of the settlement between the countries did not completely eradicate ill-feeling, there are lasting effects on their peoples.
The energy that has been needed to maintain the agreement and keep relations on track has distracted from other issues that affect the future.
And so there was still work to be done by the prime ministers of the respective countries – Japan's Fumio Kishida and South Korea's Han Duck-soo – when they met this year, first in Tokyo in March and then in Seoul last month.
The two men both braved challenging paths to get there, showing great political intelligence and courage in undertaking a task that had looked impossible for decades.
Here is a look at their diplomatic achievement and the weight of history behind it.
Colonial brutality
Han Duck-soo probably faced the more formidable challenge. South Korea suffered great and unique hardship at the hands of its neighbour.
Japanese control commenced in the mid-19th century and eventually escalated into full-scale occupation in 1910. It was to be severe and would last for three-and-a-half decades.
But Japan could not eradicate Korean identity. Even during World War II – when Japanese forces strengthened their presence and relied on local labour to assist and entertain their soldiers – the Koreans held onto their identity.
They did so despite forced labour similar to the British colonisation of Egypt and the French colonisation of Morocco. There was also a rarer colonial phenomenon: large-scale sexual exploitation.
The pain inflicted during those years remained etched in the collective memory of Koreans for generations — long after Japan's defeat in 1945 and their subsequent independence.
Transformative turning point
Losing World War II was a transformative turning point for Japan. It compelled the nation to come to terms with its colonial history by condemning it. Tokyo significantly reduced the size of its military, going as far as to reject offensive capabilities.
Japan transitioned from being one of the most belligerent nations to an admired model for others, recognised for its commitment to peace and its determination to avoid a recurrence of the bitter experiences that caused immense pain to itself and its neighbours.
On his part, Fumio Kishida faced a relatively less fraught route in Japan to bury the painful past his country shared with South Korea.
But it was far from easy. Sensitivity towards granting what the Koreans wanted – full apologies and adequate compensation – was high in certain parts of Japan's elite, and within public opinion.
The Koreans were not satisfied with the Japanese government's previous curt apology in 1992 for sexual misconduct. Nor were they satisfied with the $800 million in compensation provided by Japan in the form of non-refundable grants and soft loans, offered upon the establishment of diplomatic relations between the two countries.
Nevertheless, Kishida found an effective approach to breaking down the remaining barriers by seeking to win the hearts and minds of the Koreans.
He began his visit to Seoul by paying a visit to the national cemetery, where Korean veterans were laid to rest, and placing flowers on their graves. This gesture symbolised the deep pain he felt in his heart for the Koreans who had suffered under Japanese colonial rule.