"He is not lost to the movement, our former leaders are never lost to us," party spokesperson Jackson Mthembu told the Mail & Guardian on Tuesday night.
Motlanthe's decision not to stand for an NEC position came hours after he was defeated by president Jacob Zuma in the race to become ANC president. He lost by 2 978 votes to 991 in the election.
The move is already fuelling speculation on the sidelines of the conference that he will not remain long in government.
People close to Motlanthe told the M&G on Tuesday he was increasingly unable to contain his frustration with Zuma and may find his position untenable.
Just before the announcement Motlanthe delivered an emotional farewell to delegates and thanked the party for giving him the opportunity to serve the party.
While Zuma's supporters criticised Motlanthe for standing against Zuma, he believed that his decision was necessary in order to strengthen internal democracy in the ANC.
He wished the newly elected leaders well to carry out the mandate of the ANC to improve the lives of the poor and unite all South Africans.
"I wish you strength and wisdom in uniting the ANC and its leagues, the alliance and most important of all, all South Africans," he said.
Mthembu said Motlanthe's reasons to decline his nomination remain unclear to the ANC.
"As comrade Kgalema said, the ANC is a democratic movement and it's everybody's decision to stand or not stand for any position," Mthembu added.
As a former deputy president of the ruling party – or ex-officio member, as the ANC describes it – Motlanthe is entitled to attend all NEC meetings.
But while he is allowed to make input at these meetings, Motlanthe will have no rights to vote on any decisions made by the body.
"We would hope that he continues to play a role in the same way as former members have done and provide input to the ANC," Mthembu said.