Mangongo was only handed the reins of the national team in July, but one win in 16 matches in all formats has prompted the Zimbabwe Cricket Board to act.
A memorable victory over Australia in August was the only high point in Mangongo's time in charge, but a double whitewash in Bangladesh saw any momentum disappear.
Mangongo will now return to his position with the Under-19 side, with Zimbabwe Cricket chairman Wilson Manase believing that is his natural role.
"The Zimbabwe Cricket Board has decided to relieve Stephen Mangongo of his duties as head coach with immediate effect," said Manase. "Mr Mangongo will be re-deployed to the Under-19 setup as we believe he is good at identifying talent.
"Zimbabwe Cricket is in the process of finding a replacement coach, an announcement will be made after Christmas after interviews have been held.
"Givemore Makoni will remain as Convenor of Selectors, but will have a wider panel to select the team with. The selection panel will include Douglas Hondo as assistant/bowling coach, Babu Meman, the coach and the captain."
Zimbabwe face New Zealand and Sri Lanka ahead of the Cricket World Cup in February, where they have been drawn in Pool B.