Her resignation came less than 24 hours after the NGO - She Conquers (SC) - requested that she step down because her relationship with Zuma was “contrary to the principles and goals of the campaign”.
She had been given until April 23 to tender her resignation or face being recalled.
It is believed that the former president is the father.
Leonora Mathe, deputy chairperson of SC, confirmed that Conco resigned by mid-morning on Sunday. Efforts to get comment from Conco were unsuccessful at the time of publication.
Said Mathe: “She said she had been grateful for the opportunity, but she had decided to step down. The campaign accepted her resignation.”
SC is a national response campaign launched in June 2016 by the then deputy president, Cyril Ramaphosa. Conco was - since December 2016 - also the campaign’s treasurer and communications officer.
In its statement on Sunday, the NGO aired its apparent disapproval of the union, saying Conco had failed to disclose her relationship with Zuma. SC first learnt of the relationship through media reports on Friday.
“This affiliation is contrary to the principles that the SC campaign stands for,” its chairperson Lerato Morulane said in the statement.
“We are fully cognisant and respectful of Ms Conco’s cultural beliefs and practices However, our primary focus is putting the needs of the young people of this country in the forefront and ensuring we are not sending out contradictory messages,” she said.