Moments later, Kuala Lumpur retaliated, banning diplomats and staff at the North Korean embassy from leaving Malaysia.
The tit-for-tat moves marked an extraordinary heightening of tensions three weeks after the airport assassination of leader Kim Jong-Un's half-brother with the banned VX nerve agent.
The North decided to "temporarily ban the exit of Malaysian citizens in the DPRK", Pyongyang's official Korea Central News Agency said, citing the foreign ministry and using the North's official name, the Democratic People's Republic of Korea.
The bar would remain in place "until the safety of the diplomats and citizens of the DPRK in Malaysia is fully guaranteed through the fair settlement of the case that occurred in Malaysia".
Pyongyang and Kuala Lumpur had unusually strong links for years, but ties have rapidly degenerated in the weeks since Kim Jong-Nam was attacked at an international airport by two women using VX nerve agent, a chemical so deadly it is classed as a weapon of mass destruction by the UN.
Seoul has blamed Pyongyang for the assassination, and Kuala Lumpur wants to question several North Koreans, although the only one it arrested was released for lack of evidence.
The North has never confirmed the dead man's identity, but has denounced the Malaysian investigation as an attempt to smear it.
Kuala Lumpur announced the expulsion of the North's ambassador over the weekend. He flew to Beijing on Monday, after launching a final verbal assault on his hosts.
Kang Chol slammed what he called a "pre-targeted investigation by the Malaysian police" as he was leaving Kuala Lumpur.
Photographs later showed him sitting in the economy section of the plane.
Pyongyang retaliated by formally ordering out his counterpart - who had already been recalled for consultations.
According to KCNA, Pyongyang's foreign ministry expressed hopes that the Malaysian government would solve the issue "as early as possible" from a position of "goodwill" and "setting store by and developing the bilateral relations".
Malaysian diplomats and nationals in the North "may work and live normally under the same conditions and circumstances as before" while the travel ban is in place, it added.
It did not specify how many Malaysians are currently in the North or how long the travel ban might last.
The escalating diplomatic row already prompted Malaysia to cancel last week a rare visa-free travel deal with the North and to ban its national football team from playing an Asian Cup qualifying match in Pyongyang, citing security threats.