Former president Thabo Mbeki.
Daily Trust advisory board chairperson Salim Ahmed Salim said in a statement on Friday that Mbeki was honoured on Thursday night.
"Normally, when we as an advisory panel choose the African of the Year, we look for an ordinary African doing extraordinary things," he said.
"But this year in our deliberations we have decided to choose an already prominent African, but someone who, in the context of the Sudanese crisis, has made what we consider to be an extraordinary contribution."
In April, when Sudan and South Sudan were approaching war, Mbeki and an African Union panel negotiated between the two sides.
"For his outstanding leadership of the panel, for his persistent and consistent involvement in the peace process, and for the success of the panel in bringing Sudan and South Sudan back from the brink of war and consolidating a new start in relations, Thabo Mbeki is the 2012 African of the Year," he said.
"In honouring president Mbeki … we are not only recognising this significant achievement, but we are hoping that this will encourage the Sudanese and South Sudanese people, as well as the African Union, to stay the course on the road to a permanent peace."
President Jacob Zuma was scheduled to deliver a lecture on Mbeki in Aliwal North, in the Free State, on Friday afternoon.
The lecture forms part of a series of ANC centenary lectures on the lives of its past presidents.
Mbeki's office said he was unable to attend the event due to prior "responsibilities around the two Sudans".
In 2005 Mbeki removed Zuma from his post as deputy president, after Zuma was implicated in a corruption scandal.
Zuma later contested Mbeki for the presidency of the ANC at the party's elective conference in Polokwane in 2007 and won. Mbeki was removed from office by the ANC in September 2008 and was replaced by the now Deputy President Kgalema Motlanthe, before Zuma assumed office in May 2000. – Sapa