The region named businessperson Cyril Ramaphosa, to take over as deputy president from Kgalema Motlanthe.
Motlanthe is at the top of several regions' lists for president, but has not yet revealed whether he would accept the nomination.
The region wanted to retain Gwede Mantashe as general secretary and Baleka Mbete as chairperson.
Jessie Duarte was named to take over as deputy secretary general, while KwaZulu-Natal premier Zweli Mkhize was named treasurer general.
Regional secretary Bheki Ntshangase said eThekwini held 96 out of 103 successful branch general meetings.
Hundreds of African National Congress delegates at the eThekwini general council wore yellow and green T-shirts bearing the face of Zuma and carrying the words "100% Zuma".
The region is the ANC's biggest, with over 100 branches and more than 90 000 members.
KwaZulu-Natal is also Zuma's home province. – Sapa.