Devices issued to staff or those which are owned by employees and used for work will not be allowed to have the social media app downloaded.
The move comes as the Chinese-owned software faces intensifying scrutiny from Europe and the US over security and data privacy.
Action from the Commission follows similar moves in the US where more than half of its states and Congress have banned TikTok from official government devices.
"The reason why this decision has been taken is to... increase the commission's cybersecurity," a spokesperson said.
"Also, the measure aims to protect the commission against cybersecurity threats and actions which may be exploited for cyberattacks against the corporate environment of the commission."
Caroline Greer, TikTok's Brussels-based public policy official, tweeted that the suspension "is misguided and based on fundamental misconceptions".
Under the ban employees will be required to delete TikTok from devices they use for work by March 15.
Officials have not provided any information on how the ban will be enforced for people who use personal phones for work.
Security tensions between the West and China have become widened in recent weeks after the United States shot down a suspected spy ballon, belonging to Beijing.
Want a quick and expert briefing on the biggest news stories? Listen to our latest podcasts to find out What You Need To Know...