Sundowns booked their spot in the semi-finals thanks to goals by Peter Shalulile, Themba Zwane, Lesedi Kapinga and Hlompho Kekana while Tshegofatso Mabasa scored what proved to be a consolation goal for Pirates.
Mokoena, who spent a couple seasons as Pirates assistant, offered Sundowns technical team some insight on a few individuals.
"I think the game panned out the way we anticipated it, a lot of good work from coach Rhulani [Mokwena] in giving us better insight on individual players, their challenges and it showed immensely on the performance," Mngqithi told SuperSport TV.
"Because we knew a little bit more and areas where we can punish them, credit must be given to him for that. Coach Steve [Komphela] worked very hard to demand the press, which is what we demanded a lot from this game and the players responded.
"We should have scored more goals than what we scored, I think if I'm not mistaken I saw maybe were three or four possible penalties that we should have had, on transition we created some good moments in the first half.
"I felt very bad when we could not take the two chances that we got, with 'Mshishi' [Themba Zwane] and Peter [Shalulile] but overall I think the boys are coming very well, they're working hard defensively, they are suffocating opponents with the counter press.
"Our build-up they are a little bit more confident, it's stronger conviction in our passing game, stronger conviction in our playing angles, making sure that we always have players in the right positions," he went on.
"More especially exploiting the half spaces, I think our boys are really improving in leaps and bounds in that space. Structurally we can still improve, there are times where we don't maintain our proper structure, which makes it easier for us to break out or to play our combination plays in between or maybe interfering with our triangles.
The Sundowns co-coach also reserved special prasie for goalkeer Denis Onyango for his contribution this season.
"But nonetheless I want to give credit to our goalkeeper coach, we never really give him much credit hey. Denis [Onyango], [Ricardo] Goss, Kennedy [Mweene], Reyaad [Pieterse], even Jody [February], the improvement I see in this goalkeepers, credit must be given to this guy, he never really gets anything.
"We get so many clean sheets, we get Denis performing the way he performs at his age and we never really give him credit but I really believe today he deserves some credit, inasmuch as Denis was not really working that hard. But I just felt that we never give credit where it's due. Always keep clean sheets but he never gets anything. Today we conceded a silly goal but I'm very happy with the progress I see within the group."