James Keene's first-half goal saw the Clever Boys claim a 1-0 win over the AmaKhosi on Saturday afternoon.
"I thought the first half we didn't do well and obviously the red card we conceded changed dimensions," Komphela told SuperSport TV.
"The second half was better, we created more chances and we spent more time on their half than ours. It's just unfortunate that we have to lose matches of this calibre. But again the lesson we've learned is that the mistakes we make are very crucial we cannot afford that."
Komphela went on to explain why he brought on striker Gustavo Paez in place of defender Daniel Cardoso at the beginning of the second half.
"You had to be positive, you're losing, it's a knockout competition. You had to make a choice, you compromise one of the defenders I thought it worked well. Even when we suffered one man we could have scored here, the chance that Zuma had when he hit the crossbar and the one where he clashed with the goalkeeper. In matches of this calibre you have to take one of them," he added.
"If you're one man down, in a game of ten people and there's ten available then it means each one of us has to give an extra ten percent so we can complete the eleven on the field, so we need to create an extra player by effort. We did and it worked, I think the players did well to create that additional player we lost."