"I have come to seek your advice and your blessing," Ouattara, who is Muslim, said at the start of his meeting, which lasted around 20 minutes.
Ouattara and Benedict spoke in French without the help of interpreters.
The president, accompanied by his Christian wife and several ministers from the outgoing government, also offered the pope an ivory chess board as a gift.
Church's role
The Vatican shut down St Peter's Square for the visit - a rare measure that Italian media attributed to concern over possible anti-Ouattara protests.
Ivory Coast and the Vatican agreed on "the role that the Catholic Church can offer for the good of the country, by encouraging and promoting human rights, dialogue and national reconciliation", the Vatican said in a statement.
The talks, which included Vatican Secretary of State Tarcisio Bertone, who is effectively the pope's deputy, also highlighted the Church's role in the health and education sectors in the west African state, the statement said.
Ouattara is due to meet Italian Prime Minister Mario Monti later on Friday.
Ivory Coast's outgoing government, formed on 13 March, was led by prime minister Jeannot Kouadio Ahoussou, who also served as justice minister.
Recovering country
Ouattara has made contacts with party leaders to form a new administration, but has not given a date for the presentation of his new cabinet.
The country is still recovering from a political and military conflict in 2010-2011 when the previous ruler, Laurent Gbagbo, refused to step down even though Ouattara was declared the winner of presidential elections.
The conflict left 3 000 people dead before Gbagbo was arrested. He is now awaiting trial for crimes against humanity at the International Criminal Court in The Hague.
The Vatican has emphasised that the conflict was not inter-religious even though Ouattara comes from the north of Ivory Coast, which is majority Muslim, and Gbagbo comes from the south, which is majority Christian.
Around 40% of Ivory Coast's population is Muslim and 40% Christian. Some 20% are believers in native religions.
The 2010-201111 stand-off put the Church in a delicate position, since some bishops in Ivory Coast favoured Gbagbo. But the Church worked behind the scenes for a peaceful solution and to help internally displaced people.