Mabhudi Khenyeza scored the only goal of the game in the early minutes of the second half.
The match started with both clubs trying to get an early goal as there was not much of a difference between the ABC Motsepe team and the National First Division club in terms of their football.
In the eighth minute, Siphosakhe Mbatha had an opportunity to give his team an early lead but decided to blow it away as Arrows Keeper Mbaeva made a save.
It was Natal United that attacked more and added pressure on the former Absa Premiership club Golden Arrows in the middle of the park.
Just five minutes before the half time, Chris Katjuikua of Golden sent his free header over the crossbar, missing out an opportunity to score the first goal of the match.
In the second half Golden Arrows took control in this match as they dominated the court.
Former Bafana Bafana player Mabhudi Khenyeza pulled a long shot from range to test the Natal United goalkeeper Nkosingiphile Zondi, but the shot-stopper managed to get hold of it.
Five minutes later Khenyeza came back again and this time he found the back of the net and took his side to a 1-0 lead in the 53rd minute with his ground shot.
After this goal Arrows attacked more from both sides, but the Natal United goalkeeper Nkosingiphile Zondi was well alert.
Andile Fikizolo also came close to doubling the score for Arrows, but his well-placed shot just went inches away from the right pole.
This saw the Arrows defending the 1-0 lead until the match was over and advancing through to the quarter-finals of the Nedbank Cup.