Oscar Mabuyane has retained his position as Eastern Cape provincial chairperson.
Mabuyane, who held the position of provincial chairperson and convenor, faced off against former provincial treasurer Babalo Madikizela.
He obtained 812 votes against 662 cast for his rival in a heavily contested election.
Voting got underway early in the morning after an intense standoff on the credentials.
Mlungisi Mvoko was elected as the deputy chairperson.
President Cyril Ramaphosa is set to address the conference during its closing later today.
The ANC started its conference on Saturday with an address by national chairperson Gwede Mantashe.
President Cyril Ramaphosa was supposed to deliver the closing remarks on Sunday, but this was moved to Monday after delays.
The ruling party spent Sunday dealing with the issue of credentials and planned to finish the conference on Monday.
The party was stuck on the question of credentials of some of the branch delegates for hours on Sunday until they were adopted by delegates.
More than 1 300 voting delegates took part in choosing the five leaders to lead the province and the Provincial Executive Committee (PEC).
The battle for control of the party had been intense with both sides pushing hard for their candidates.
ANC NEC deployee Dr Aaron Motsoaledi said they had to attend to some serious issues raised at the conference.
“The issues there were about the authority of the court about Rubusana,” said Motsoaledi.
This related to the judgment on Saturday that rejected an urgent application by some of the members to exclude some of the branches from the Dr BW Rubusana region.
Motsoaledi said this was one of the sticking points but the conference eventually forged ahead.