The ABC Motsepe League side lost 2-0 via goals either side of the break from Mandla Masango and Aubrey Modiba at Sugar Ray Xulu Stadium last night.
"I'm very happy with the performance of the boys tonight... obviously I'm disappointed with the result but I believe the difference between us and them is that they took their chances and we didn't take ours," Ngubane said after the game.
"I think that was the only difference in the game because, when you look at the goals that they scored, it was not from open play but it was from our mistakes."
The former Royal Eagles boss hopes their run in the competition can serve them in their push for a play-off spot with six games to go in the third tier.
"We still have a big one coming up on Saturday against Uthongathi, the log leaders in the ABC Motsepe League. So taking this performance into that game it'll also help us on preparations in the next coming games. It is only six games to go now before we finish the season.
"So we learnt a lot from this tournament: number one, some of my players it was the first time they were playing in the night game, and for them to play against the defending champions in the Nedbank Cup and the team that is challenging the league title in the PSL and giving such a performance, I believe we did very well."