Franck Kessie and Sebastien Haller got the goals for the host nation after Player of the Tournament William Troost-Ekong had given Nigeria a first-half lead.
Seko Fofana and Serge Aurier also featured for Ivory Coast in Sunday's final, while 2023 African Footballer of the Year Victor Osimhen was on the losing side.
These two teams had met earlier in the tournament when Nigeria won 1-0 during the group phase.
It was Ivory Coast's third title after wins in 1992 and 2015, both won on penalties.
MNA