Sundowns were held to a 1-1 draw at the FNB Stadium on Saturday after needing a win to progress to the competition's semi-finals after a 2-1 first-leg defeat.
Speaking after the final whistle, Mngqithi admitted his side came up short in reaching their end-of-season targets.
"We were a bit unfortunate that we didn't qualify for the semi-finals," Mngqithi said post-match. "But I think the boys gave a good account of themselves.
"It's probably us as the leadership that will have to take the bullet and say maybe we need to plan and do better in the next coming matches and make sure that we improve in this space because seemingly we are not achieving our ultimate goals.
Mngqithi also gave credit to the opposition who nullified the widely-regarded tournament favourites.
"We were playing a very good team," Mngqithi added.
"One must not take that away from them, but the number of chances that we created does suggest that we dominated the game.
"We could have easily scored two or three goals in the first fifteen minutes, we created very good chances, but unfortunately when you don't take those early chances in the match and as the game progresses you start getting anxious.
"I would give them credit because they've gone through, but I wouldn't really think that their organisation made it very difficult for us to penetrate and create clear cut opportunities which I believe we created."