The decision leaves Cyril Ramaphosa, the clear favourite, to run against Mathews Phosa and Tokyo Sexwale for the position.
Fikile Mbalula will run against the pro-Zuma Gwede Mantashe for secretary general.
Another pro-change candidate, Thandi Modise, who is the incumbent deputy secretary general and premier of the North West province, withdrew her bid to keep her current party job. Her strategy mirrors Motlanthe's, she will now stand only against Baleka Mbete for national chair, leaving Jessie Duarte, who is on the Zuma slate, to run unopposed for deputy secretary general.
And Sexwale withdrew from consideration as treasurer general, leaving his pro-change counterpart, Paul Mashatile, to contest Zweli Mkhize alone.
Sexwale's nomination as deputy president presents a small vote of confidence for a leader who has been frank – if unsuccessful – in his presidential ambitions.
But the position of deputy president, which will set the tone for the ANC's choice of president in 2017, is likely to go to heavyweight contender Cyril Ramaphosa, even though Ramaphosa's recent involvement in the Marikana mine shooting left a cloud hanging over his reputation.
Ramaphosa, who sent an email to Police Minister Nathi Mthethwa appealing for action against the miners days before the incident, remains a non-executive director of Lonmin – the mine where the shooting took place.
But Ramaphosa is still widely respected in ANC circles and has a strong political track record as the ANC's chief negotiator during talks to end apartheid. He was also instrumental in the drafting of South Africa's Constitution.
And based on the numbers, Phosa and Sexwale will have a tough time standing against Ramaphosa.
Ramaphosa received close to 2 000 provincial nominations for the post, while Phosa and Sexwale received just 385 and 419 respectively.
The lukewarm delegate response to the announcement of their nominations casts further doubt on their success.
Ramaphosa's nomination announcement was met with thunderous applause and cheers from the delegates, while Sexwale and Phosa both received muted responses.
Throughout the process candidates from the Zuma slate drew by far the loudest cheers from the floor.
Free State premier and longtime provincial chair Ace Magashule said the outcome of the elections was almost obvious based on the delegates' reaction to the announcement of each nominee's name.
"People have made up their minds. I have been in the ANC long enough to read the signs."
He said he was satisfied with how the nomination process went.
His provincial executive committee lost a court case to disgruntled ANC activists and now has to hold fresh elections in three months. Magashule declined nomination as national chair.
Action now moves to the voting hall, where delegates will be forbidden from bringing in cellphones or cameras in a bid to ensure that they do not send confirmation of their votes to anyone outside the process.
ANC president (2):
ANC deputy president: (3)
Baleka Mbete (declined)
Kgalema Motlanthe (pulled out)
National chairperson (2):
Ace Magashule (pulled out)
Thenjiwe Mtintso (pulled out)
Secretary general (2):
Deputy secretary general (1):
Thandi Modise (pulled out)
Treasurer general (2):
Tokyo Sexwale (pulled out)