Khuliso Mudau opened the scoring at Loftus Versfeld with 35 minutes on the clock. There was a brief VAR review but the goal was awarded with Mudau adjudged to have been onside when he collected the ball.
Brayan Leon added a second goal ten minutes into the second half, and substitute Iqraam Rayners fired home in the 74th minute for a comprehensive victory, with his goal also the subject of a VAR review.
Njoya was convinced the two goals should not have been allowed, as his team now face a mountain to climb heading into the second leg at home this Friday.
"There is so much progress to make in the level of VAR because we [conceded] two goals, which are not goals – referee denied goals, but VAR said it's a goal," said Njoya on African Football.
"I think it was wrong when, you know, Mamelodi Sundowns players are putting pressure on the referee. I think it should not be happening," added Njoya, who also conceded that Sundowns were the better team.
"I don't know if VAR was working perfectly. It looked like it was not working perfectly. But overall, I can say the Mamelodi Sundowns deserved the win."
When asked if his side have a change to overturn the first-leg deficit, the coach added: "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."
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Mamelodi Sundowns coach Miguel Cardoso welcomed the use of the Video Assistant Referee (VAR) after his side secured a convincing 3-0 victory over Stade Malien in the first leg of their CAF Champions League quarter-final clash.
