The Tshwane giants found their way back into the match early in the second-half through an equalizer by captain Hlompho Kalake and with substitute Thapelo Morena grabbing the winner in the late stages of the game.
Bongani Chakile put the lower division side ahead in the 16th minute to stun the premier league leaders who squandered a lot of chances in the opening minutes of the game.
“It is always scary when a small team is leading at that time of the game, but we had to be careful because if you go out they will catch you on the counter-attack,” Mngqithi said during the post-match interview.
“The first half should have been a different story; we made a stupid mistake and got punished immediately for it.
“We created a lot of chances and we could have taken the lead, even from the first half. No wonder the goalkeeper was the man of the match; he kept them in the game.”
Mngqithi said he was aware that Bees were going to get tired in the second- half and they would use their experience to find their way back.
Sundowns were without head coach Pitso Mosimane away in Rabat, Morocco to complete his Pro License.