The visit, just weeks before Japan's most controversial premier steps down from power, once again demonstrated Mr Koizumi's Janus-faced nature: a conservative whose mantra is "reform without limits"; a man who talks endlessly about the future but who sometimes seems held in thrall to the past.
The visit also demonstrated his skills as a master of the media theatre, but yesterday's piece of political kabuki could cost Japan dearly. The pilgrimage to the most contentious piece of real estate in Asia ends Mr Koizumi's five-year premiership on a bitterly divisive note and worsens ties with China and South Korea, which both reacted furiously.
Across Asia, Yasukuni symbolises Japan's undigested history and its lack of contrition for an imperialist war that killed millions of Chinese, Korean and other civilians. Ironically meaning "peaceful nation", the 10km
2 plot of hallowed ground was directly run by the military during the Second World War. Millions were trained to fight to the death and told that the highest honour for a soldier was enshrinement there as a kami, or god. "See you at Yasukuni" became a famous wartime slogan.
The US postwar occupation divested the shrine from the state and put it under the management of a private religious organisation. But with the names of 2.5 million dead listed in its Book of Souls, Yasukuni remained a potent symbol for nationalists even before the secret decision in 1959 by the Shinto priests to begin enshrining Class B and C war criminals, convicted by an Allied military tribunal. In 1978, the priests listed the 14 men who had led the war, including Prime Minister Hideki Tojo, among the shrine's list of official deities. At a stroke, they removed one of the central planks of Japan's post-1945 settlement with Asia: the separation of the wartime leadership from the rest of the "brainwashed" population. Politicians who went to the shrine would now be implicitly honouring the wartime leadership - and by extension, the war - along with ordinary soldiers.
When the enshrinement was leaked to the press in 1979, it caused uproar in China and Korea and even upset Emperor Hirohito, who thereafter refused to visit Yasukuni. Several leaders made pilgrimages after 1979, some in secret, but Prime Minister Yasuhiro Nakasone's decision to go on 15 August 1985, the 40th anniversary of Japan's surrender, sparked such a furious reaction abroad that no Japanese leader dared visit on that date again - until yesterday.
Later, at a ceremony to mark the end of the war, Mr Koizumi apologised to Japan's war victims, saying: "Our country caused huge damage and suffering to a number of countries."
The apology, first issued more than a decade ago by the socialist prime minister Tomiichi Murayama amid intense opposition, has since become Tokyo's boilerplate response to claims it has not properly atoned for the war.
Nationalists have waited since 2001 for the prime minister to fulfill a pledge to visit Yasukuni on 15 August, which Japan calls "end of the war day". Critics say the semantic sleight of hand allows Japan to avoid using the more contentious terms "surrender" or "defeat" and implies that the war was a natural disaster that befell the country, like an earthquake or a typhoon.
"Japanese pacifism is based on victimisation so we can't use any words that suggest we were actively involved," said Koichi Nakano, professor of comparative politics at Tokyo's Sophia University. "Japan never talks about people killing and doing awful things. This visit takes this process a step forward because it contributes to the blurring of war responsibility even further."
The controversy over how Japan chooses to remember - or forget - the Pacific War - is stoked by the refurbished 4bn yen (£18m) museum just yards from the shrine's inner sanctum where Mr Koizumi signed his name in a visitor's book. The museum audaciously rewrites the history of the conflict, arguing that the invasions of China and Korea were "defensive". Visitors to the museum learn that Korea, which was occupied for half a century by Imperial Japan, was a "dagger pointing at Japan's heart"; that China prolonged the war unnecessarily by not coming to terms with their conquerors; and that 200,000 slaves forced to service wartime troops - the so-called "comfort women" - were "prostitutes". Thousands of men who climbed into kamikaze planes and torpedoes to immolate themselves against the hulls of American warships are venerated in photographs and pseudo-religious testimonies. The museum entrance is dominated by a black locomotive used to pull trains along the Burma railway, which took the lives of thousands of Allied prisoners of war. No mention is made of these deaths.
For Tetsuro Kato, professor of politics at Tokyo's Hitotsubashi University, Yasukuni is "doubly offensive" because it was designed to mobilise Japanese to kill and to die and because it shows Japan has never come to terms with defeat. "The shrine and the attached museum still maintain it was a defensive war," he said. But ultra-conservatives, including Mr Tojo's granddaughter Yuko, claim it is no worse than other war memorials around the world, including Arlington Cemetery in the US.
Recent polls show a majority of Japanese are against annual prime ministerial visits to the shrine, although many cite Japan's tattered relations with its Asian neighbours rather than Yasukuni's skewered take on history. The anti-Yasukuni faction has been swelled during recent years by some unlikely recruits, including the families of the Class A war criminals, eight of whom say they don't care whether their souls are enshrined there or not.
The visits are also opposed by much of Japan's business community, which fears their impact on Tokyo's business ties, and by Takenori Kanzaki, the leader of Mr Koizumi's coalition partner, the New Komeito party, who called the trip "regrettable".
But the perils of publicly criticising the shrine were highlighted when the home of the ruling Liberal Democratic Party bigwig Koichi Kato, was firebombed after he suggested the visits should be "reconsidered".
The pilgrimages play well, however, with Mr Koizumi's conservative base and will add to his political legacy - one month before he steps down - as a maverick prepared to challenge taboos. Some of Mr Koizumi's colleagues are desperately searching for a solution to the shrine issue before it seriously damages Japan's economic relationship with China. The Finance Minister Sadakazu Tanigaki is one of several ministers who believes the shrine should separate the war criminals from the rest of the dead.
All eyes are now on Mr Koizumi's successor, most likely Chief Cabinet Secretary Shinzo Abe, who secretly visited the shrine in April. Mr Abe refused to say whether he would go as prime minister, repeating earlier statements that "misunderstandings" with China and South Korea "need to be removed".
Enshrined: Japanese war criminals
Hideki Tojo
Prime Minister for most of the Second World War, widely regarded as the chief architect of Japan's wars against China, Korea and the Allied forces.
Koki Hirota
Responsible for planning Japan's invasion of China as Prime Minister prior to Tojo. Convicted of war crimes.
Iwane Matsui
Led the attacks on Nanjing in 1937, where up to 20,000 women may have been raped by Japanese troops.
Doihara Kenji
Approved the Japanese attack on Pearl Harbour. A veteran spy, nicknamed "Lawrence of Manchuria" for his knowledge of the province he planned for years to invade.
Akira Muto
Under his command, Japanese forces in the Philippines executed and tortured thousands of civilians.
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