The cabinet confirmed on Thursday that Dr Nkosinathi Sishi is the new DG of Higher Education.
Qonde and Higher Education Minister Blade Nzimande were later embroiled in a legal battle after the former challenged his suspension from the department.
But he lost the case in the Labour Court in Joburg.
Nzimande, when he suspended Qonde two months ago, said this was based on the disclaimer of the Auditor-General Tsakani Maluleke.
Nzimande said he also welcomed the finding of the court that ruled in his favour.
Qonde had argued that his suspension by the minister was unlawful.
Qonde had been in the department for more than a decade and was part of it when it was formally separated from basic education to form two different departments of education.
This had followed a resolution of the ANC in Polokwane in 2007 that education must be split into two.
When the new administration took over in 2009 higher education and basic education became standalone departments with two ministers.
Nzimande had insisted that he had done nothing when Qonde was suspended a few weeks ago.
But the former DG said the suspension was unlawful and he lost his bid in court.
The former DG was suspended in July and he took the matter to the Labour Court in August, but the ruling went against him in September