The hosts scored both their goals in the first half – through Katlego Mphela and Bernard Parker.
Bafana were certainly the dominant team in the opening 45 minutes as they controlled the midfield battle and dictated the possession stakes.
The home side attacked from the first whistle, with Parker almost opening the scoring in the third minute when he met the end of a right wing cross, but his header was brilliantly saved by Daouda Kassali.
Still, Bafana only had to wait another nine minutes before they did take the lead through the dangerous Mphela.
The goal was created by Steven Pienaar, who won the ball in midfield and then played Mphela through on goal with just the keeper to beat. The Sundowns striker showed good composure to chip the goalie and give his side the lead.
The only chance on goal for Niger in the first half came in the 18th minute when Moussa Maazou tested Bafana’s Itumeleng Khune from about 25 yards out, but it was a comfortable save.
Mphela nearly doubled his side’s lead in the 36th minute when he showed strength to win the ball in midfield and proceeded to beat one defender and again left himself with just the keeper to beat. This time, however, Kassali produced a good save by spreading himself well to block the shot.
South Africa continued to press forward and did eventually find their second goal three minutes into added time of the first half.
Anele Ngcongca drove down the right flank, beating one defender before supplying a teasing cross into the 18-yard area. Parker then did brilliantly in the middle of the box, stopping in his tracks and producing an acrobatic scissor-kick to fire the ball home.
The second half continued where the first left off as Bafana were unrelenting in attack and went in search of their third goal.
And they nearly found it in the 55th minute. Pienaar was at the thick of the action again this time supplying a through ball for Parker, but he failed to beat the goalie, who produced a good low save to his right.
It was almost the exact same move three minutes later, this time Pienaar playing Siphiwe Tshabalala through on goal, but he too squandered a golden chance, chipping the ball over the crossbar.
Pienaar was the heart of the South African team on the night as he was the source of great playmaking. He also nearly found his name on the score sheet in the 72nd minute, but Kassali was again at his best, diving full stretch to his right to tip away an 18-yard shot.
Bafana continued to press forward but try as they might the South African team could not find their third goal as the game finished 2-0 in their favour.
It was a well deserved victory for South Africa as Niger were virtual spectators for the entire 90 minutes. Still, Bafana coach Pitso Mosimane will be delighted with the three points and a convincing win.