He said he would ask the International Criminal Court to probe massacres in which both his forces and those of his rival Laurent Gbagbo were suspected.
Mr Gbagbo was captured on Monday by Mr Ouattara's forces after he refused to accept he lost elections in November.
He will now face charges at a "national level and an international level", Mr Ouattara said.
At a news conference in the main city of Abidjan, Mr Ouattara said Mr Gbagbo had been moved to a secure location.
During the four-month stand-off between the two rivals for the presidency about 1,500 people were killed and a million forced from their homes.
The UN says fighting and looting continue in the country and aid agencies say the situation for civilians is dire, with shortages of food, water and basic services.
The international community, including the UN, recognised Mr Ouattara as the election winner, but Mr Gbagbo said the vote was rigged.
The conflict threatened to plunge the world's biggest cocoa producer back into civil war, with Mr Ouattara's supporters controlling the north and Mr Gbagbo's in control of the south.
Truth and reconciliationMr Ouattara said the justice minister was preparing a case against Mr Gbagbo, but he would be treated with respect.
Some Gbagbo supporters were attacked after he was captured on Monday "There will be charges on a national level and an international level," he said.
"Gbagbo is in a residence under surveillance somewhere in Ivory Coast," Mr Ouattara told reporters at the Golf Hotel, where he has made his headquarters during the crisis.
"Mr Laurent Gbagbo is a former head of state, he must be treated with consideration."
The UN said its peacekeepers in Ivory Coast had transported Mr Gbagbo to the north and were providing security for him.
The ex-president had first been taken to the Golf Hotel after Mr Ouattara's forces, with French support, had removed him from the presidential palace.
Mr Ouattara said he had phoned South Africa's President Jacob Zuma for advice about setting up a credible and independent truth and reconciliation committee.
It would be asked to consider atrocities from the 1990s to the present day.
"Reconciliation has to happen with justice," he said.
Sheltering in a churchMr Ouattara said he would be moving in a few days into the presidential palace and that a formal presidential swearing-in ceremony would follow.
Footage of the moment Laurent Gbagbo was detainedThe Constitutional Council, run by an ally of Mr Gbagbo, had sworn him in as president in December, after annulling thousands of pro-Ouattara votes.
The country's security and resuming cocoa exports would be top priorities, the new president said.
"We need to secure the country, notably Abidjan," he said. "It is important for the country to emerge from this crisis on top."
Exports of cocoa, the West African nation's main foreign revenue earner, could be resumed immediately, he said.
Human rights group Amnesty International had earlier called on Mr Ouattara to end reprisal killings against those seen as Gbagbo supporters.
It said some pro-Ouattara forces were going house-to-house in Abidjan, abducting and killing people.
It also said some 27,000 people were still sheltering in a church in the western town of Duekoue, where hundreds of bodies have been found after pro-Ouattara forces advanced on Abidjan from their northern strongholds earlier this month.
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