The decision came after reports that Zuma had won wide support from ANC provincial branches and was leading incumbent Mbeki ahead of a December congress that will choose new party leadership.
"The margins are very close ... out of 54 votes, current president Thabo Mbeki got 25 votes and comrade Jacob Zuma got 29 votes," ANC Women's League President Nosiviwe Mapisa-Nqakula told delegates after the vote.
Traditionally, the ANC president would also become the national president in elections scheduled for 2009 because of the party's grip on South African politics.
Mbeki cannot be re-elected as South Africa president but would retain much power and have a hand in selecting his successor should he win next month's ANC election.
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