The Shinto shrine in Tokyo honours 2.5 million war dead, including 14 convicted war criminals.
China and South Korea in particular see Yasukuni as a symbol of Japan's past militarism and see visits to it as a lack of understanding or remorse over wartime history.
Two photos removed from Instagram showed Bieber praying outdoors at the shrine and standing beside a Shinto priest.
The images outraged China as well as many Instagram and Twitter users.
In a new Instagram post, Bieber wrote that he asked his driver to stop at the shrine but was misled on its purpose.