At least three people were killed and both sides have said some of their supporters were prevented from voting. The first results are expected later on Monday with the electoral commission under pressure to release them quickly. A night-time curfew has been imposed and will run until Wednesday, following incidents of violence during the campaign.
UN envoy to Ivory Coast Youn-jin Choi said three people had been killed but said the violence was "localised" and overall the voting had taken place in a "democratic climate", reports the AFP news agency.
A government official earlier said two people were shot dead by traditional hunters in the centre-west cocoa-producing region amid clashes between rival supporters on voting day.
This area is seen as a potential flashpoint, as the local community mostly back President Gbagbo, who is from their Bete ethnic group, while most of those who work the fields have migrated to the area from other parts of the country where support is strong for Mr Ouattara.
Ivory Coast is the world's largest cocoa producer and used to be considered a haven of peace and prosperity in West Africa.
Mr Ouattara's RDR party has said pro-Gbagbo youths set up road-blocks to prevent his supporters and election agents reaching polling stations in parts of the centre-west. But the Dozo hunters who allegedly shot dead one soldier and a civilian are considered to be close to the northern New Forces ex-rebels, who Mr Gbagbo's supporters say are linked to Mr Outtara.
