Jean, who was born in Haiti and left with his family to New York when he was nine, maintains that he meets the necessary residency requirements to run for president.
Although Jean and his lawyers have said they will appeal in court, paperwork has not yet filed. It is also unclear if an appeal is even possible under Haitian law.
Jean was among 34 people considered by the body but was left off the list of approved candidates.
Haiti was hit by a devastating earthquake on January 12 that killed at least 250,000 people and left 1.5 million homeless.
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.
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.