Disgruntled soldiers mutinied in the city of Bouake on Friday, with troops in other cities joining the uprising.
Defence Minister Alain-Richard Donwahi was also briefly seized by mutineers after he went to Bouake to negotiate.
The mutiny, over pay, ended when Mr. Ouattara agreed to demands.
A statement from the president's office on Monday said army chief Gen Soumaila Bakayoko, gendarmerie commander Gervais Kouassi, and director-general of the police Bredou M'Bia had been relieved of command with immediate effect.
The statement did not mention the reason for their removal.
The mutiny began in Bouake early on Friday with soldiers firing rocket launchers.
Protests also took place in the cities of Man, Daloa, Daoukro, Odienne and Korhogo and on Saturday soldiers took over the army headquarters in Abidjan.
President Ouattara went on national television on Saturday night to announce a deal had been struck.
"I confirm that I have agreed to take into account the demands of the soldiers over bonuses and better-working conditions," he said.
Aside from better pay, the agreement was reported to include an amnesty for the mutineers.
The mutiny raised fears of a resurgence of the violence seen during Ivory Coast's 10-year civil war, which ended in 2011.