Algeria, Ghana and Nigeria all paid the price for the uncertainty that has come with recent coaching changes while the Ivory Coast and Cameroon were also unimpressive as they looked to a new post-World Cup era.
Only hosts South Africa seem to have kicked on from the tournament they hosted in June and July, springing to the top of the qualifying group they share with African champions Egypt.
Algeria's 2-0 defeat on Sunday away against the lowly ranked Central African Republic was one of the biggest upsets in Nations Cup qualifying history.
It marked only the second time the Central African Republic, who rarely enter the tournament and have only ever played in a single World Cup qualifying campaign before, had won a competitive international. Their last success was in 1973.
Algeria now have just a single point from their opening two 2012 Nations Cup qualifiers after being held at home by Tanzania last month in another upset result.
It led to the resignation of coach Rabah Saadane.
The tenure of his successor Abdel Benchikha could be over after just a single game in charge with Algerian newspapers speculating on Monday he will be replaced this week.
"I was shocked with just how average the Algerian team looked," Frenchman Jules Accorsi, the coach of the Central African Republic, told reporters after the match in Bangui.
INSTABILITY
Both Ghana and Nigeria have yet to appoint new coaches after their World Cup managers moved on and the instability showed on Sunday. Nigeria's 1-0 loss in Guinea was exacerbated by the uncertainty of the status of the game up until Friday.
Nigeria were suspended last week by FIFA for political interference in the running of their football association, leaving the team's preparations in limbo until Friday when the ban was temporarily lifted.
Ghana played a first match since coach Milovan Rajevac departed to a more lucrative club job in Saudi Arabia and also looked lacklustre in a goalless home draw with Sudan, a side they had dispatched with some ease both home and away last year in the qualifiers for the 2010 World Cup finals.
Cameroon's qualification chances took a knock on Saturday in a tough group they share with Senegal and the Democratic Republic of Congo.
A first home game for new coach Javier Clemente ended in a 1-1 draw with the Congolese, allowing Senegal to go to the top of the group standings.
The Ivory Coast continue to battle without the presence of Didier Drogba, who has taken time off from the national side after the World Cup. They managed a pedestrian 1-0 win in his absence over Burundi on Saturday.
