The 3-0 result leaves the Malian champions facing an uphill task in next week’s return leg in Bamako, where they will need at least three goals without response to force the tie to penalties.
Two of Sundowns’ goals were initially flagged offside before being overturned by the VAR officials – decisions that frustrated Njoya.
"There is so much progress to make in the level of VAR because we take two goals, which are not goals – referee denied goals, but VAR said it's goal," bemoaned Njoya.
"It's not the end of the world, we are going to play them in Bamako. I think they have scored three goals here, we can score three goals too, why not? We can score, we are not crying about that."
The Cameroonian tactician also dismissed the notion that Sundowns proved to be more experienced than they were to see the game through, and vowed to be better in the second leg.
"I think I have given more points to Mamelodi Sundowns to avoid what you are saying, it's not because of their experience or because they were stronger than us," he defended.
"I think that it's football, it can happen, and we think the next match will not be the same as this, I promise you that we are going to win the match in Bamako – even 3-0 to go to penalty kicks, or I don't know, but we have to score many goals."