The official, who requested anonymity, told The Anadolu Agency on Wednesday that Bahah had left for a "safe location" after leaving the presidential palace.
On Tuesday, violent clashes erupted between presidential guard units and militants from the Shiite Houthi movement, which had earlier captured the presidential palace in Sanaa.
The Houthis have remained in control of Sanaa since last September. They have since moved to extend their influence to other provinces, especially in central Yemen.
President Abd Rabbuh Mansur Hadi is currently inside his home in downtown Sanaa.