Emmet Doyle was selected to replace Dr McCloskey by party members on Thursday.
He unsuccessfully sought election as an SDLP candidate to the council in 2014 and again in 2019 as an independent candidate.
Mr Doyle said he was “humbled and excited” to have been ratified by the party.
“I want to use my experience in the political life of our city to fight for adequate housing, community infrastructure and secure jobs for the future,” Mr Doyle said.
Mr Doyle, at one-time an advisor to former Foyle SDLP MLA Pat Ramsey, added: “Our community deserves nothing less.”
Dr McCloskey stood down earlier this month due to differences of opinion with her party over Stormont’s handling of Covid-19.
She also stood down as deputy leader but remains a party member.
However, she has not ruled out running to be elected an MLA in the future.
Founded by ex-Sinn Féin member Peadar Tóibín, Aontú has two councillors in the North of Ireland.
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