The visit would be within the context of South Africa's commitment to strengthening bilateral economic relations with Namibia and within the broad framework of advancing the African agenda, the department said in a statement on Monday.
Mbeki and Namibian President Hifikepunye Pohamba would preside over a review of progress on strategic projects between the two countries.
The department said the commission's discussions would focus on, among other things, trade and industry, agriculture, energy, the environment and tourism, science and technology, and transport and communication.
"Since the establishment of the economic bilateral commission, South Africa has assisted Namibia to establish a cardiac unit at the Windhoek Central hospital," the department said.
"On 23 June 2008, Namibia opened its first cardiac unit and became the third country on the continent after South Africa and Egypt to have a cardiac unit and to conduct successful heart operations."
Namibia was also an important global partner in the Square Kilometre Array project, which South Africa made a bid for in May 2003.
Both countries had agreed to continue cooperating in capacity building in the area of astronomy and astrophysics.
"In this regard, the National Laser Centre in South Africa is working closely with the Faculty of Science at the University of Namibia in developing a laser and photo laboratory."
The department said bilateral trade between South Africa and Namibia accounted for two-thirds of Namibia's total foreign trade.
The countries' strategic relations were further enhanced by their membership of the Southern African Customs Union and the Common Monetary Union.
South Africa and Namibia were also part of the Southern African Development Community economic partnership agreement configuration which was negotiating with the European Commission.
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