Council spokesman Richard Dumel said election officials have accepted 19 candidacies and rejected 15 others. The Haitian-born singer's candidacy was turned down because he did not meet the residency requirement of having lived in Haiti for five years before the Nov. 28 election.
Jean, whose parents brought him to the United States as a child, has lived off and on in Haiti in recent years. In 2007 he was named roving ambassador to Haiti by President Rene Preval, an appointment he says qualifies him to run for president of the country.
Crowds had gathered outside the council's office before the decision was announced late Friday. The decision had already been postponed once this week.
Supporters of the former Fugees frontman had said before the ruling that they suspected members of Haiti's political elite are trying to block his campaign.
Ahead of the expected ruling, Jean moved from a compound outside the capital to a hotel around the corner from the electoral commission and his family issued a statement saying he was still hoping that he would be accepted as a candidate either later Friday or over the weekend.
Jean, who gained famed as a member of the hip-hop musical group Fugees before building a solo career, has no political organization, not much of a following beyond his fans of his music 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.
He also has faced persistent criticism over alleged financial mismanagement at the charity he founded, Yele Haiti.
On the other hand, he has generated global attention to a race in which almost no one outside Haiti could even name any of the candidates.
"If he hadn't been involved, today, no one would be talking about candidates in the Haitian presidential election," said Mark Jones, a professor of political science at Rice University in Houston.
The 40-year-old singer's fame and wealth instantly made him a formidable candidate in the desperately poor Caribbean nation he left as a boy - though some Haitians question the seriousness of his run.
"I don't think he's a politician at all," said Etienne St. Cyr, a pastor who helps at a camp for homeless earthquake survivors at the Petionville Country Club. "Maybe he's not what we need right now."
St. Cyr said Jean has not won over the people camped in squalid tents on the slope of a golf course, noting they already have allegiances to established political parties and the singer has not visited the camp.
Analysts say it is difficult to assess what kind of support Jean has beyond his mainly young and urban fans, but as a well-funded wild card, he has made more-established politicians nervous. Earlier this week, Jean said he had received death threats from somebody who called and told him to get out of Haiti.
The winner of the Nov. 28 election will take charge of Haiti's earthquake recovery, coordinating billions of aid dollars in a country with a history of political turmoil and corruption. January's earthquake killed an estimated 300,000 people and left the capital, Port-au-Prince, in ruins.
The devastation from the earthquake, coupled with frustration over a weak government response, have created an opening for a messianic outsider like Jean, said Robert Fatton Jr., a Haiti expert at the University of Virginia.
"The very fact that he is taken seriously when, in fact, he has no preparation to be president is an indication that the whole country, in particular the youth, looks at the typical Haitian population as a bankrupt kind of species," Fatton said.
Melia reported from San Juan, Puerto Rico. Associated Press Writer Chris Gillette in Port-au-Prince contributed to this report.