Head of technical affairs Jan Pruijn will be in charge for the League match against AmaZulu on Saturday, assisted by Wilfred Mugeyi.
According to club CEO George Comitis the decision to fire the coach had to be taken sooner rather than later.
"As of today, coach Maarten Stekelenburg will no longer be the head coach of Ajax Cape Town," Comitis said.
“We had to make a change before it was too late. Sometimes you have to shake everything up.
“Irrespective of whether we gave him an ultimatum we believe we need a more experienced coach because he is dealing with more experienced players."
Comitis says Stekelenburg "lost the belief of the board and directors", although he still had the support of his players.
"The players will be sad, they were behind MS all the way and felt it was their duty to make things right," Comitis admits.
Comitis adds that Ajax have made no decisions about a new coach yet, although Foppe de Haan's name has been mentioned.
"We would look at bringing back someone like Foppe, but we have made no inroads to a decision as of yet."
"We will sign someone on an interim basis if that is the case. It's a big decision so we need to make the correct choice.
"We won't be going into the market for new players and we don't want a coach that isn't focused around our youth system!"
De Haan led Ajax to a second-position finish in the League in 2011.