Attorney-General Mark Dreyfus said the decision followed advice from the country's intelligence agencies and would begin "as soon as practicable".
Australia is the last member of the secretive Five Eyes security alliance to pursue a government TikTok ban, joining its allies the United States, Britain, Canada and New Zealand.
France, the Netherlands and the European Commission have made similar moves.
Dreyfus said the government would approve some exemptions on a "case-by-case basis" with "appropriate security mitigations in place".
Cybersecurity experts have warned that the app -- which boasts more than one billion global users -- could be used to hoover up data that is then shared with the Chinese government.
Surveys have estimated that as many as seven million Australians use the app -- or about a quarter of the population.
In a security notice outlining the ban, the Attorney-General's Department said TikTok posed "significant security and privacy risks" stemming from the "extensive collection of user data".
China condemned the ban, saying it had "lodged stern representations" with Canberra over the move and urging Australia to "provide Chinese companies with a fair, transparent and non-discriminatory business environment".
"China has always maintained that the issue of data security should not be used as a tool to generalise the concept of national security, abuse state power and unreasonably suppress companies from other countries," foreign ministry spokesperson Mao Ning said.
- 'No-brainer' -
But Fergus Ryan, an analyst with the Australian Strategic Policy Institute, said stripping TikTok from government devices was a "no-brainer".
"It's been clear for years that TikTok user data is accessible in China," Ryan told AFP.
"Banning the use of the app on government phones is a prudent decision given this fact."
The security concerns are underpinned by a 2017 Chinese law that requires local firms to hand over personal data to the state if it is relevant to national security.
Beijing has denied these reforms pose a threat to ordinary users.
China "has never and will not require companies or individuals to collect or provide data located in a foreign country, in a way that violates local law", the foreign ministry's Mao said in March.
- 'Rooted in xenophobia' -
TikTok has said such bans are "rooted in xenophobia", while insisting that it is not owned or operated by the Chinese government.
The company's Australian spokesman Lee Hunter said it would "never" give data to the Chinese government.
"No one is working harder to make sure this would never be a possibility," he told Australia's Channel Seven.
But the firm acknowledged in November that some employees in China could access European user data, and in December it said employees had used the data to spy on journalists.
The app is typically used to share short, lighthearted videos and has exploded in popularity in recent years.
Many government departments were initially eager to use TikTok as a way to connect with a younger demographic that is harder to reach through traditional media channels.
New Zealand banned TikTok from government devices in March, saying the risks were "not acceptable in the current New Zealand Parliamentary environment".
Earlier this year, the Australian government announced it would be stripping Chinese-made CCTV cameras from politicians' offices due to security concerns.
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