Both countries have stopped the transfer of funds by those suspected of financing North Korea's weapons programme.
Australia's foreign office released a list of 11 companies based in Pyongyang, North Korea's capital, a Swiss company and a Swiss-based businessman that Australians are banned from doing business with.
Alexander Downer, Australia’s foreign minister, said: "We will implement similar sanctions against any other companies or individuals who seek to undermine international security and stability through assisting North Korea continue its ill-considered, costly and provocative WMD [weapons of mass destruction] programmes."
Japan's sanctions affect 15 groups and one individual, including 12 North Korean trading houses and one bank, the government said in a statement. Those singled out would need to obtain government permission to remit or withdraw money from Japanese bank accounts.
Shinzo Abe, Japan's chief cabinet secretary and leading candidate to be the next prime minister, said: "This shows the resolve of the international community and Japan."
The measure follows a United Nations resolution which was passed after North Korea defied international warnings and test-fired seven missiles into the sea in July.
The UN Security Council voted unanimously for the resolution which demanded that North Korea halt its ballistic missile programme, and required other nations to prevent Pyongyang from acquiring dangerous weapons.
Japan reacted angrily to the North Korean missile tests, saying that Pyongyang's arsenal posed a threat to its security.
A ferry that provides the only direct passenger link between the two countries was banned from its ports for six months and North Korean government officials were refused entry.
Pyongyang agreed a year ago to dismantle its nuclear programme in return for aid, security assurances and improved diplomatic ties, but it has refused to return to the talks with China, Japan, Russia, South Korea and the US since last November.