The Chinese foreign minister Wang Yi summoned the Japanese ambassador on Thursday to lodge "strong opposition" to the visit, China's official Xinhua news agency reported.
The incident has prompted a message of concern from the United States about deteriorating ties between the North Asian neighbours. The US has expressed disappointment that "Japan's leadership has taken an action that will exacerbate tensions with Japan's neighbours," the according to a statement by the US embassy in Japan.
China and South Korea have repeatedly expressed anger in the past over Japanese politicians' visits to the Yasukuni Shrine, where Japanese leaders convicted as war criminals by an Allied tribunal after World War II are honoured along with those who died in battle.
The two countries have been especially touchy about visits to the shrine by serving Japanese prime ministers, and Abe is the first leader in office to pay homage at Yasukuni in the past seven years.
Business ties between China and Japan, the world's second- and third-largest economies, have improved after a downturn sparked by a flare-up last year in a row over tiny East China Sea islands controlled by Japan but also claimed by China. But worries are growing that an unintended incident between Japanese and Chinese aircraft and ships playing cat-and-mouse near the disputed isles could escalate into a military clash.
Abe, a conservative who took office for a second term exactly one year ago, said he did not intend to hurt feelings in neighbouring nations. "There is criticism based on the misconception that this is an act to worship war criminals, but I visited Yasukuni Shrine to report to the souls of the war dead on the progress made this year and to convey my resolve that people never again suffer the horrors of war," he told reporters after the visit.
Television carried live video of his motorcade making its way to the shrine, built in 1896 by Emperor Meiji to enshrine war dead. Yasukuni played a key role in the wartime state Shinto religion which mobilised the population to fight in the name of a divine emperor.
Abe, dressed in a morning suit and a silver tie, bowed at the shrine before following a Shinto priest into an inner sanctum. Stressing that it was natural for a nation's leader to pay his respects to those who died for their country, Abe said: "I have no intention to hurt the feelings of the Chinese or Korean people."
Abe also said he shared the view of past Japanese leaders who had paid their respects at the shrine that ties with China and South Korea were important and that to make them firm was in Japan's national interests - and said that he would like to explain that if given the opportunity.
A "brazen" act
Tokyo's relations with Beijing and Seoul are already strained by territorial rows and disputes stemming from Japan's wartime occupation of large parts of China and its 1910-1945 colonisation of the Korean peninsula.
For many in China and South Korea, Yasukuni remains a symbol of Japan's military atrocities. Among those honoured there are 14 World War Two leaders convicted by the Allied tribunal as "Class A" war criminals, including then prime minister Hideki Tojo. A museum in the shrine's grounds depicts the Pacific war as one Japan was forced to fight in self-defence and has been criticised for ignoring the atrocities Imperial Japanese troops committed in Asia.
China's foreign ministry swiftly called the visit a "brazen" act. "The Chinese government expresses strong indignation at the Japanese leader's trampling on the feelings of the people of China and the other war victim nations and the open challenge to historical justice... and expresses strong protest and serious condemnation to Japan," it said.
A commentary in state-run news agency Xinhua added: "Choosing a sensitive time to visit a highly controversial and notorious place, Abe knows perfectly what he is doing and the consequences. Instead of a pledge against war, as Abe has claimed, the visit is a calculated provocation to stoke further tension."
In an e-mail sent to Japanese nationals registered with the Japanese embassy in Beijing, the embassy warned its citizens to stay away from any demonstrations and to not congregate in big groups.
"Given the media coverage, we fear the deterioration in sentiment towards Japan," the embassy said. "In dealing with Chinese people, pay attention to your behaviour and your language."
South Korea termed the visit a deplorable and anachronistic act that damaged ties between the two countries and summoned a top Japanese diplomat in Seoul to protest. "We cannot withhold regret and anger over the visit," said Minister of Culture, Sports and Tourism Yoo Jin-ryong.
Washington - which has welcomed Abe's more proactive defence policies but been unhappy at his historical revisionism - also expressed disappointment. "Japan's leadership has taken an action that will exacerbate tensions with Japan's neighbours," a US Embassy statement in Tokyo said. "The United States hopes that both Japan and its neighbours will find constructive ways to deal with sensitive issues from the past, to improve their relations, and to promote cooperation in advancing our shared goals of regional peace and stability."
The head of Abe's coalition partner, the Buddhist-backed New Komeito - who had urged the premier not to make the pilgrimage - called the visit regrettable in light of the problems it as likely to cause with Japan's neighbours.
Impact of visit unknown
Japanese exports to China have recovered after a sharp drop following scattered protests in China in 2012. That was sparked by Japan buying disputed East China Sea isles that are claimed by both countries to fend off a bid by the then-governor of Tokyo, a nationalist, to purchase them. It was unclear whether Abe's Yasukuni visit, the first by a serving premier since 2006, would dampen business ties again.
"We don't know how much impact the visit might have. I hope this will not develop into a huge problem." Kyodo news agency quoted a Japanese car company executive as saying.
Former Prime Minister Junichiro Koizumi's annual visits to Yasukuni during his 2001-2006 tenure were a major factor in the chill in ties between Japan and its Asian neighbours. Abe, who succeeded Koizumi in 2006, stayed away from Yasukuni during that term and repaired frayed ties with China with a summit. But he later said he regretted not visiting Yasukuni as premier.
Paying respects at the shrine is part of Abe's conservative agenda to restore Japan's pride in its past and recast its wartime history with a less apologetic tone. He also wants to ease the restraints of Japan's post-World War Two pacifist constitution on the military.
Some political experts said Abe had probably calculated that his relatively high voter ratings, based largely on hopes for plans to revive the economy, could withstand any criticism over his Yasukuni pilgrimage, which would also shore up support in his conservative base. He may also have felt that with ties with Beijing and Seoul in a deep freeze, a visit would hardly make things worse.
"He probably thinks that it's OK, that's he's relatively popular and it's a matter of conviction," said Koichi Nakano, a professor at Sophia University in Tokyo. "But everyone knew with Koizumi ... he wasn't a revisionist nationalist. But with Abe, that is precisely the question some people were asking. Now we know the answer."