The Black Management Forum (BMF) was left without a managing director last year after Nicholas Maweni fell out with president Bonang Mohale‚ while Nomaxabiso Majokweni resigned as Business Unity South Africa's (Busa) chief executive last week.
BBC's secretary Sandile Zungu confirmed that Qubeka would leave at the end of February after serving his two-year contract.
"A succession plan is underway and we are currently searching for a new chief executive‚" he said.
It is understood Qubeka will join the Recycling and Economic Development Initiative of South Africa (Redisa)‚ a non-profit organisation, which aims to develop a sustainable South African tyre recycling industry through an integrated industry waste tyre management plan.
The national tyre recycling plan sparked controversy a year ago over concern that prices may be set centrally for an industry worth more than R600m. Redisa is an affiliate of the council.
Zungu said the council is looking for the "best of breed" leader to take the organisation forward. "That the leader should not have an adversarial posture towards government‚ but rather understand the art of engagement and be passionate about the interests of our membership," he said.
"These are very exciting times for black business‚" he added.
Since its launch in March 2012 - when it had just more than 20 members - the council has grown to more than 50 members.
The Black Management Forum led the walkout of black business from big business's umbrella body‚ Busa‚ in 2011‚ accusing it of failing to look after black business interests.
The drive to create a united‚ single business body received a fresh push after Busa said last week it was refocusing its efforts to become that body.
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