Cherif Ousmane, the commander of Ivorian forces, was quoted by the BBC as saying the business district in Abidjan was "now definitively occupied by us."
Forces loyal to Ivorian leader Laurent Gbagbo clashed with Ouattara supporters for months following a November presidential election meant to united a country divided by civil war in 2002. Gbagbo refused to step down despite overwhelming international support for his rival.
At least 1,000 people were reportedly killed in the unrest and tens of thousands of people were displaced to neighboring Liberia. Gbagbo was arrested in April.
Ivorian Prime Minister Guillaume Soro said the streets of Abidjan were still "littered with bodies."
Andris Piebalgs, the European Union's commissioner for development, is to meet Friday with Ouattara in Abidjan to discuss his support for at least $130 million in reconstruction projects.
"I made the commitment to come to Ivory Coast at this early stage after the end of the severe crisis in order to express the European Union's support for the country and its government in re-establishing its political stability, democratic order and economic strength for the benefit of the population of Ivory Coast," Piebalgs said in a statement from Brussels.