Sundowns raced to a 4-0 lead in the first half-an-hour thanks to goals by Peter Shalulile, Lebohang Maboe, Lesedi Kapinga and Andile Jali.
However, the Brazilians took their foot off the gas in the second stanza and Mngqithi was not happy with the performance of second-half substitutes.
"I think we started the game very well, we put the right intensity anf forced them into making errors, managed to score four goals first half," Mngqithi told SuperSport TV.
"Then decided to give other players a chance and rest other players we need for the game against Stellenbosch, unfortunately when you take out so many of our regular players, the game never looked the same.
"We never looked threatening, I even doubt we had more than two shots at goal in the second-half, it was very disappointing to be honest because when you give an opportunity to somebody who has not been playing you expect him to exert himself and show that he really deserves to be in the team," he said.
"Hindsight will say, 'Ey maybe I should have given others a chance' but it's always fair to give other boys a chance and see what they can offer.
"Maybe we can say they didn't perform at the level we wanted but the good thing is that now they know there is a lot that is expected from them and they must give their best shot," he went on.
"But I must be honest, second-half I was not happy at all. I wanted more. I wanted the team to score as many goals as possible, for that is always important to score when you've got a chance because it builds the confidence of the team but unfortunately we didn't do that but nonetheless, it was still a good game."
The former Golden Arrows mentor was asked if they get enough time to train given their hectic schedule and also touched on the subject of a quarter-final meeting with Orlando Pirates.
"It's a little bit tough but at least we're used to it now, our best training sessions are our matches that's where we train a lot and during the week maybe we have regeneration day and one training match, minus one if we're fortunate it or match day minus three, which is good but we never really get much time to train in season," he said.
"Our periodisation is always more on trying to make sure that the team is fresh for the next match and when you score early, it gives you that opportunity to take some players out and possibly have a better team for the forthcoming game.
"But the truth of the matter is in season Sundowns never really gets to train, maybe we train with video analysis and other things but the physically we don't want to..."
"I don't even want to focus on the Pirates game at this stage, our main focus at this stage is the game against Stellenbosch because we have to take each game as it comes, not think about other bigger games that are coming and end up not collecting points where you have to collect points.
"So our target at this point is to do what we can to collect maximum points in Cape Town, it's always one of those bafana skin games but we'll do the best we can we're confident the team can deliver that we expect."