Following the final whistle, Mnqithi hit out at Chiefs for hosting Pitso Mosimane's side at their Naturena training base ahead of Saturday's encounter.
"For me, winning this was sweeter because I felt Chiefs was being spiteful by allowing Al Ahly against us.
Ngwenya labelled Mnqithi's swipe at Chiefs as unnecessary following an impressive 1-0 win over Al Ahly in the CAF Champions League at FNB Stadium on Saturday.
The win virtually secures the Brazilians' passage to the competition's quarter-final stage with 10 points after four matches played.
"Honestly I think he could have gone without talking about that," Ngwenya tells KickOff.
"I mean he overshadowed the good result over Al Ahly with what he said.
"I think it's something he could have left out, I mean Sundowns did well to seal the double over Al Ahly.
"We should be celebrating but now there's too much focus over other things off the field.
"I think it overshadows this good result, I think he would have done better not to speak about that or entertain it.
"Honestly I don't think there's anything wrong with what Chiefs did and Al Ahly is allowed to use Chiefs' facilities.
"I'm sure they are not the worst facilities, so I don't think it was anything wrong and it was just business.
"So Mnqithi shouldn't have spoken about it."