Under a presidential decree, General Hussein Naji Hadi Khairan replaces Ahmed Ali al-Ashouel, who moves to the Majlis al-Shura (consultative council), the lower chamber of parliament.
No reason was given for Hadi sacking Ashouel late on Sunday.
But it comes with the impoverished Arabian Peninsula state embroiled in political and military chaos and Ansarullah delaying a pullback it agreed to under a UN-brokered accord in September.
The Huthi militia swept south from its rugged northern stronghold to capture Sanaa before then extending its influence into central and west Yemen.
The unopposed Ansarullah offensive meant it was able to take over several government arms depots including those housing heavy weapons.