South Africa took time to settle and struggled with possession early in the game, as they could not complete more than five passes going forward.
However, Nigeria failed to take advantage of that, because they kept possession in their own half and were often given no space in front of the Bafana goal.
Nnamdi Oduamadi came close and nearly gave Nigeria the opener in the 11th minute after the Bafana defence allowed the Super Eagles to play the ball behind them, but Itumeleng Khune was quick to react and stopped Oduamadi.
Tokelo Rantie and Bernard Parker combined well in the 16th minute, but Rantie was tightly marked as Bafana could only settle for a corner which resulted in open play.
Bafana launched another attack a few minutes later, but Thuso Phala’s cross could not find Reneilwe Letsholonyane as Nigeria recovered in time to clear their lines.
The home side came close in the 24th minute, but Parker’s low from inside the Nigeria box was too strong for Siphiwe Tshabalala.
Sunday Mba should have done better in the 25th minute after some exciting combination with Ogenyi Onazi, but his poorly taken shot was easily saved by Khune.
John Ogu nearly put Nigeria in front with a cheeky chip in the 26th minute, but his attempted shot hit the cross bar and went over with Khune well beaten.
Rantie tried his luck from distance moments later, but the Super Eagles keeper Austine Ejide made a comfortable save.
Khune had to make a difficult save to deny Victor Obinna in the 33rd minute, as Nigeria looked to break the deadlock before half time.
Khune again denied the Super Eagles the opening goal with a fine save in the 42nd minute, after well taken shot by Ogu from outside the Bafana penalty area.
Rantie had a chance to put Bafana in the lead a few seconds later, but his shot hit the wrong side of the net.
Bafana should have been 1-nil up on the stroke of halftime, but Letsholonyane was wasteful from Parker’s low cross, as the dreadlocked midfielder had too many touches inside the Nigeria box.
Bafana had a brighter second half start and won a free-kick on the left hand side of the Nigerian box in the 46th minute after a foul on Parker, and the Chiefs hitman dusted himself up to whip in a beautiful cross that was punched away by Ejide, but the Super Eagles keeper made amends to deny Thabo Nthethe with a brilliant save, as Bafana won an early corner.
Nigeria then took the lead through substitute Uche Nwofor with a cheeky finish in the 48th minute after the Bafana defence was caught napping.
South Africa tried hard to get the equalizer, but they often lacked composure as they blasted most of their chances over the bar.
Stephen Keshi introduced Chelsea’s Victor Moses after the hour-mark and the Nigerian forward changed the complexion of the game with his dangerous runs.
Uche Nwofor broke South Africa’s hearts with an easy tap-in in the 67th minute after a skilful display from the Nigerians split the Bafana defence to eventually beat the helpless Khune.
Substitute Lerato Chabangu saw his long range shot sail over the bar, as he looked to catch Ejide off-guard for Bafana’s first goal against Nigeria in nine years.
The home side won a free-kick outside the Nigeria box in the 77th minute, but Parker’s well taken free-kick was too strong as it sailed over the bar.
Bafana pressed forward in the dying minutes of the game, and won a free-kick on the edge of the Nigerian box, but Tshabalala’s attempt was deflected for a corner.
Ahmed Musa came close in the 90th minute with a brilliantly played cross which nearly beat Khune, but it flashed across the face of goal.
Tshabalala had his shot blocked by Ejide, as the Super Eagles held on to their 2-0 lead to be crowned the Nelson Mandela Challenge champions.