Jean was among 34 people considered by the body but was left off the list of approved candidates which was published last week.
The singer-songwriter's candidacy had been challenged over the requirement that everyone who runs must have lived in the country for five years before the November 28 election.
Jean has argued that he was not required to comply with the law so strictly because after President Rene Preval appointed him as roving ambassador in 2007, he was allowed to travel and live outside the country.
Some officials in Haiti worried about political unrest among Jean supporters after his candidacy was rejected.
But the singer asked his fans to stay calm, and there were no significant election-related protests or violence over the weekend - although rumors swirled about a large protest planned for Monday.
|Jean had been criticised for a lack of political experience and a vague platform [EPA]
In a open letter released before the decision was announced, Jean, who moved to the United States when he was nine years old, said that whatever his fate the world needed to do more to help Haiti.
"We need the attention of a world that cares for humanity and the dignity of a race and culture," he said.
Haiti was hit by a devastating earthquake on January 12 that killed at least 250,000 people and left 1.5 million homeless.
Jean said in the letter that he would ask each member of the Haitian diaspora, estimated to number more than one million people in the US and Canada alone, to contribute $10 to rebuilding their homeland.
The hip-hop star's application to stand in the race had been criticised by those who questioned his political experience and accused a charity he runs of misusing donations.
He had no political organisation and only a vague platform, casting himself as an advocate of Haiti's struggling youth and saying he will ask reconstruction donors to help the country's dysfunctional education system.
However, Jean is hugely popular among Haiti's youth and about 300 of his supporters marched in heavy rain outside the country's electoral office in the capital Port-au-Prince on Thursday.
Haiti's new president will be taking charge of the earthquake recovery, co-ordinating billions of aid dollars in a country with a history of political turmoil and corruption.