The ruling deals a final blow to Sonko's presidential aspirations, hampered by a flurry of court cases that have piled up against him since he was accused of rape in 2021, spurring violent protests across the country.
Although he was cleared of the rape charge, Sonko has been found guilty of libel and an offence described in the penal code as immoral behaviour towards individuals younger than 21.
He was arrested in July for insurrection and struck off the electoral role, but still submitted his candidacy from prison after a court in the south of Senegal ruled in his favour.
Ly did not provide a reason for the council's decision to reject Sonko's application.
The Feb. 25 election is a "joke because everything is opaque, it lacks transparency," he said via telephone.
The legal saga embroiling the popular opposition politician has fuelled several bouts of sometimes deadly unrest over the past two years - damaging Senegal's reputation as one of West Africa's most stable democracies ahead of the poll that will determine President Macky Sall's successor.
Sonko denies any wrongdoing and says all charges against him are politically motivated. The government denies this and accuses Sonko of stoking violence. It dissolved his Pastef party in July.
A former tax collector with a populist rhetoric, Sonko came third in Senegal's 2019 presidential election, garnering an unexpectedly high number of votes for a first-time runner.
Particularly popular among disillusioned urban youth, he had become the voice of frustrations over economic hardship and lack of jobs that marred Sall's popularity over the course of his two terms in office.
Applications to run in the presidential election are currently being reviewed ahead of a Jan. 20 deadline to publish a final list of cleared candidates.
Sall in September named Prime Minister Amadou Ba as the ruling coalition candidate.
Amid Sonko's legal travails, one of his close allies, Bassirou Diomaye Faye, has applied to run as an independent candidate.
(Reporting by Portia Crowe and Diadie Ba Writing by Sofia ChristensenEditing by Mark Potter)
