Mali, who finished third at the African Nations Cup finals earlier this year, lost 1-0 away to Benin in their opening group game while Libya kept up their recent heroics with a 1-1 draw in Togo.
There was a dramatic late equaliser for Uganda as they salvaged a point in Angola in one of seven African qualifiers played on Sunday.
It completed a weekend of 20 matches at the start of the group phase of qualifiers for Brazil where little went with the form book.
Ike Uche delivered a rocket-like shot 10 minutes from time to spare Nigeria potential blushes against Namibia after he had earlier missed a host of good chances in Calabar.
It was modest 1-0 win for a country, whose population of more than 150 million contrasts starkly with the 2 million Namibians, but will be welcome by new coach Stephen Keshi, seeking to rebuild their team after missing out on qualifying for the 2012 Nations Cup finals.
South Africa admitted under-estimating opponents Ethiopia in their Group A game in Rustenburg and emerged with a fortuitous 1-1 draw after Katlego Mphela equalised in the 77th minute.
"Our guys thought it was going to be easy but we must give our opponents credit. Maybe this is a wake up call," said South Africa's beleaguered coach Pitso Mosimane.
Ethiopia, who had only won once in 16 previous World Cup qualifiers on the road, had taken the lead through Said Saladin on the half-hour mark.
Razak Omotoyossi scored the only goal in Cotonou as Benin overcame Mali in Group H.
Any hopes Mali had of building on their surprise semi-final spot at the Nations Cup have evaporated in recent months after a military coup and the subsequent insecurity prompted FIFA move their home game to neutral venues and coach Alain Giresse depart.
Libya, in contrast, continued their fairytale progress of the last two years despite also being forced into both preparing and playing outside of their country.
Under new coach Abdul-Hafeedh Arbeesh, they battled out a draw in Togo, who were World Cup finalists six years ago.
Togo, playing again without Emmanuel Adebayor, scored first through Kalen Damessi but Libya were level inside the opening quarter-hour through Ahmed Zuway.
Emmanuel Okwi provided an 87th minute equaliser as Uganda pulled off a 1-1 draw away against Angola, another country who played in Germany in 2006.
A free kick from Ibrahima Traore saw Guinea beat Zimbabwe 1-0 away while Gabon drew 0-0 in Niger.