Zimbabwe Cricket (ZC) said the changes were made keeping in mind the team's poor performance in the ICC World Twenty20.
Zimbabwe crashed out in the preliminary stage of the ICC World Twenty20.
Bowling coach Ntini will take over the charge as interim coach from Australian Whatmore, who was handed a four-year contract in April last year.
"Head coach Davenell Whatmore has had his contract terminated with immediate effect. Bowling coach Makhaya Ntini has taken over in an acting capacity until the appointment of a substantive head coach," a statement from ZC said.
Zimbabwe have also signed former South Africa all-rounder Lance Klusener as batting coach for two years.
Zimbabwe will play India in three One-Day Internationals and as many Twenty20 Internationals, starting June 11 at the Harare Sports Club here.