Nees had been in the job for 14 months, ensuring Zimbabwe's qualification for the Cup of Nations finals in Morocco.
He then oversaw the last six matches of the 2026 World Cup qualifying campaign, in which they ended last in their group, having drawn three and lost three.
Overall, he won two of 14 games he was in charge of since being appointed in August last year.
Zimbabwe must now find a new coach in time for the Cup of Nations, where they face Egypt in their opening Group B game in Agadir on December 22, and Bafana Bafana seven days later.
The 58-year-old Nees had previous national team jobs in Africa with Seychelles and Rwanda and was technical director in Israel and Kosovo.