The Southeast Asian nation joins countries around the world that have limited travel from southern Africa, where the variant, believed to be the most contagious yet, was first detected.
The travel ban applies to eight African countries, including South Africa, Zimbabwe, Mozambique and Malawi, but could be extended to other nations where the variant has been detected, such as Britain and the Netherlands, health minister Khairy Jamaluddin said.
Malaysia will also delay plans to set up so-called Vaccinated Travel Lanes (VTL) with the affected countries, and reimpose quarantine requirements for Malaysian citizens and long-term residents returning from those nations, regardless of their vaccination status.
"These are just temporary measures until we find out more about the Omicron variant," Khairy said.
"The moment we believe it is safe, we will lift these measures."
Malaysia, which has reported more than 2.6 million coronavirus cases, has gradually reopened its borders to travelers in recent weeks as infections have slowed amid a high vaccination rate.
Earlier this week, Malaysia and Singapore launched a two-way joint VTL, reopening their border after nearly two years during the pandemic.
(Reporting by Rozanna Latiff; Editing by Martin Petty)
