South Africa, on their part crashed out of the tournament, as Mali overpowered Mozambique 2-1 to top the group and also book their passage to the last eight.
Bafana Bafana needed only draw the game to make sure of their quarter-final place, and eliminate Nigeria in the process, but continue their poor string of results against the Super Eagles.
They finished third in the group behind Nigeria and Mali, who now advance to the last eight.
Much more embarrassingly this side bore no resemblance to the Nigeria team that won the African Nations Cup last year while South Africa’s side had several of its established internationals.
Nigeria’s goals came from diminutive winger Chrisantus Ejike and an Ifeanyi Ede penalty.
The first two were as a result of defensive errors. The opening goal saw the back four out of position as Ede played a square pass in for Ejike to tuck away in the 22nd minute.
The second goal was an error from Moeneeb Joseph, who had replaced injured captain Itumeleng Khune in goal, as he let an innocuous ball spill out of his hands and then, as he tied to retrieve the loose ball, brought down Nigeria’s Fuad Salami. Ede converted the subsequent penalty to leave the Cape Town Stadium shell shocked after 32 minutes.
South Africa did conjour up chances for Siphiwe Tshabalala and Bernard Parker and were denied a chance to pull back one goal the hour mark when Nigeria’s goalkeeper Chigozie Agbim pulled of a brilliant stop to deny a curling effort from Katlego Mashego, who was brought off after just 35 minutes to bolster the Bafana attack.
But any hopes of a comeback were thwarted by a brilliant goal in the 64th minute when a swift one-two involving Ejike and Salami saw the small winger crash home a stunning goal.
Nigeria’s Rabiu Ali struck the cross bar with a swirling over-the-shoulder effort in the 71st minute
Solomon Kwambe picked up a second caution and was sent off for the last quarter-hour but the advantage for Bafana was lost within two minutes when Vuyo Mere was cautioned for a second time for a mistimed tackle and also had to go for an early shower.
The consolation only came in the 81st minute when Bernard Parker tucked away a penalty after the referee awarded for a tackle by Azubuike Egwuekwe on Mashego in the box.