The constitutional council also barred former president Laurent Gbagbo and former rebel leader turned prime minister Guillaume Soro from standing in next month's presidential election.
It cleared only four of the 44 candidates for the October 31 presidential election.
The other candidates cleared were former president Henri Konan Bédié from the historically dominant PDCI party, Gbagbo's former prime minister Pascal Affi N'Guessan, and Kouadio Konan Bertin, a dissident from Bédié's party.
In the economic capital Abidjan, protesters torched a bus in the working-class district of Yopougon, an AFP photographer said, after scuffles broke out earlier in the day between security forces and youths.
The district is thought to be a fiefdom of exiled former president Gbagbo, whose supporters had filed an application for him to run in the vote.
It was Gbagbo's refusal to concede defeat to Ouattara after the 2010 election that sparked the bloody conflict in the former French colony, formerly a beacon of stability and prosperity in the region.
In the centre-west city of Bangolo, demonstrators set fire to a mining truck and other vehicles on Monday, according to a resident who requested anonymity, and who added that gendarmes dispersed them with tear gas.
Witnesses said security forces took down barricades set up by protesters on several roads in the west of the former French colony.
Around 15 people have died in violence since Ouattara, 78, announced last month that he would run for a third term.
Gbagbo sentenced in absentia
Although the constitution limits presidents to two terms, Ouattara and his supporters argue that a 2016 constitutional tweak reset the clock.
The president had previously committed to not running again, but he changed his mind after the sudden death of his anointed successor, prime minister Amadou Gon Coulibaly, from a heart attack in July.
The electoral commission has said that anyone convicted of a crime will be disqualified from running for the top office and barred Soro from running as he was sentenced in April to 20 years in prison for "concealment of embezzlement of public funds".
Gbagbo has been sentenced in absentia to a 20-year term over the looting of the local branch of the Central Bank of West African States during the 2010-11 crisis.
Former president Bédié is expected to be the opposition's mean flagbearer, after his PDCI party nominated the 86-year-old as its candidate on Saturday.
At a rally attended by tens of thousands of supporters in the capital Yamoussoukro, Bédié pledged if elected to work for "the unconditional return of all exiles, as well as the release of all political, civilian and military prisoners from the post-election crisis".
Bédié is seeking to return to the presidency after he was ousted in the country's first coup in 1999.
(FRANCE 24 with AFP)