Mr Koizumi spent about 10 minutes inside the shrine
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Fourteen war criminals including wartime Prime Minister Hideki Tojo are honoured there among 2.5m war dead.
China said Mr Koizumi’s visit offended victims of past Japanese militarism and South Korea also voiced disapproval.
It was Mr Koizumi’s first to the Yasukuni shrine on an anniversary of Japan’s surrender in World War II.
Mr Koizumi arrived in a limousine and entered the huge shrine behind a Shinto priest in traditional robes.
He spent about 10 minutes inside and left white chrysanthemum flowers with a donor’s plate which read "Prime Minister Junichiro Koizumi", AFP news agency reports.
Yasukuni supporters, including a number of right-wing activists in military fatigues, waved Japanese flags as Koizumi visited.
"Mr Koizumi, thank you!" supporters shouted as he left.
‘Hurt feelings’
The visit was guarded by hundreds of police backed by helicopters.
Anti-shrine demonstrators have been holding a vigil in Tokyo
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Opponents of the visit earlier held candlelight vigils and marches, drawing supporters from Taiwan, South Korea and all over Japan.
China’s foreign ministry said Beijing had "strongly protested" against Mr Koizumi’s visit for "wrecking the political foundations of China-Japan relations".
"Prime Minister Koizumi has constantly on historical issues hurt the feelings of the Chinese people…" a statement said.
South Korea’s foreign ministry expressed "deep disappointment and anger" over the visit, according to The Associated Press.
Both South Korea and China have suspended summit meetings with Mr Koizumi since his last visit, in October.
Wooing conservatives
Mr Koizumi brushed off the criticism, telling reporters that his visit had been "appropriate".
"I made the visit to show respect and appreciation to those who offered their lives for the sake of the country and to their families," news agency AFP quoted him as saying.
Mr Koizumi has visited the Yasukuni Shrine every year since he became prime minister five years ago but always stayed away on 15 August.
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YASUKUNI SHRINE
 Built in 1869 to honour victims of the Boshin Civil War
Now venerates the souls of 2.5m of Japan’s war dead
Those enshrined include 14 Class A war criminals
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When he was trying to win the leadership of his party five years ago he promised he would visit the Yasukuni Shrine on the anniversary of the end of the war, says the BBC’s Chris Hogg in Tokyo.
That promise won him crucial support from more conservative elements within his party, our correspondent says.
Attention has also been focused on the stances of potential contenders to succeed Mr Koizumi.
The front-runner, Chief Cabinet Secretary Shinzo Abe, who has visited the shrine in the past, has declined to say what he would do if he becomes prime minister.
Leading rival Sadakazu Tanigaki has ruled out a visit and Foreign Minister Taro Aso, another contender, is also thought to be against one.
Public concern over the shrine issue has been increasing, with recent polls suggesting more than half the Japanese public do not want their next prime minister to continue the visits.
On Sunday, more than 1,000 people marched in Tokyo to protest against visits to the shrine.
