Provinces calling for a second term for Zuma have endorsed Kgalema Motlanthe or NEC member Cyril Ramaphosa as deputy president.
The nomination and voting process was still not underway at midnight on Friday.
ANC provincial chairperson Marius Fransman said the verification of 21 branches caused the delay to the start of the Provincial General Council (PGC).
Some delegates fell asleep in the almost empty University of the Western Cape lecture hall where voting was to take place, while others sang and danced outside the hall.
The Western Cape has 170 branches.
Only 150 qualified to attend the PGC, because they had, according to rules, held their branch general meetings to nominate a delegate to attend Mangaung.
Divided
Earlier in the day, delegates appeared divided on who they wanted to see as ANC president at Mangaung.
Some sang pro-Zuma songs and wore t-shirts depicting his face. Others wore sweaters with the words "anti-tribalism" printed on them as well as a list of their top six for the ANC. This included Kgalema Motlanthe for president, Mathews Phosa for deputy president and Tokyo Sexwale for treasurer general.
Across the country other provinces carried out the nomination process, with Northern Cape and Eastern Cape nominating Zuma to stand for a second term. The process was not so smooth in Limpopo.
According to provincial secretary Soviet Lekganyane the nomination was disrupted on Friday evening.
"Delegates have been invaded by hooligans," he said.
"The situation is potentially dangerous."
Verification of delegates
Lekganyane said the police were called, but an hour later had still not arrived.
The conference was supposed to have started on Friday morning with registration at 8am. Proceedings were delayed because of problems with verification of delegates. By 6pm only two of Limpopo's five regions had been verified.
Earlier this week, the province had to postpone its nomination conference at the last minute to allow branches to complete their general meetings. They were given until Friday to do this.
This was also the deadline, set by the ANC's national executive committee, for nominations.
Limpopo's regions differed in their nomination of who should lead the party for the next five years. Some wanted Zuma to retain his position while others wanted deputy president Motlanthe to take the reins.
Four names have emerged as favourites for deputy president. Provinces calling for a second term for Zuma have endorsed Motlanthe or NEC member Cyril Ramaphosa as deputy president.
Those who wanted Zuma replaced backed Sexwale or Phosa.