International relations spokesman Clayson Monyela said the summit on Wednesday and Thursday would afford Africa and Europe the opportunity to cement bilateral political and socio-economic co-operation.
Leaders of the two continents would review progress in the past three years under the Africa-EU Action Plan 2010-2013 adopted in Libya.
It was expected the summit would discuss the financing of priority projects in Africa.
Nkoana-Mashabane was expected to hold talks with her counterparts from Africa and Europe on the sidelines of the summit.
Monyela said on Monday that President Jacob Zuma would not attend the event because he had other commitments.
Zimbabwean President Robert Mugabe called for a boycott of the summit after his wife, Grace, was refused a visa to attend. The couple have been banned from visiting the European Union because of their alleged role in rights abuses, but as head of state Mugabe is still allowed to attend international forums.