Following the 2-0 loss to his former club, Mokwena conceded his players failed to capitalise on key opportunities earlier in the group phase that ultimately left them with too much to do in their final fixture.
According to the coach, arriving at Loftus Versfeld needing at least a point against a determined Sundowns outfit was always going to be a tall order.
"We didn't get knocked out today. If you review our participation in the Champions League, we maybe let it go when we were away in Rwanda," said Mokwena.
"Conceding first, making it 1-1 and then in the last 10-12 minutes to lose 2-1 away from home – when you have a point away in the Champions League, it's very important.
"And then at home we had a lot of chances against Sundowns, and it's important to win your home matches in the Champions League, and we took a point when we could have taken three, and that would have made a big difference.
"And then Lupopo in Congo, 0-0 with the last few minutes and we concede a penalty that we could have done better – and even though when I reviewed the game I don't know how much of a penalty that should have been.
"But if you review how we've done in the Champions League this season, and we've spoken about this, I don't think this was the game that got us knocked out of the group stages."
Mokwena was asked whether being eliminated from the Champions League would affect his job security at Mouloudia.
"I don't know, that's up to the club. I'm focussed on what's left of the remainder of the season, that's a question that's not within my control," he responded.