Eagles held Chiefs to a goalless draw in the first stanza, but Lebogang Manyama found the winner for Amakhosi with 20 minutes remaining.
Mohafe felt Khama Billiat's inclusion was key to changing the game for the Absa Premiership leaders as his players started leaving gaps.
"A good game of football, we started by defending deep and waiting for them, denying them those spaces behind the defence, denying them the spaces in front of goals, hoping to catch them on a counter," Mohafe said on SuperSport TV after the match.
"We did so, they missed us in several occasions, we should have scored, they should have scored in the first half. But first-half mission accomplished, we just wanted to frustrate them a bit, we did that. We accomplished that.
"And we see how good can we defend against Chiefs and we take it to the league. Second-half, just a bit of the boys cramping but you still need to say because they're cramping, what do I do next?
"Can you change the plan? You can't change the plan because whenever they are cramping, it means they are going to leave those spaces we're denying Chiefs," he went on.
"Okay, fair enough, they brought in [Khama] Billiat with the speed and they catch us with the speed behind the defence, that's how they scored.
"I can't blame the boys for the effort, they gave a good account of themselves and for us, a blessing in disguise, we'll concentrate more on the league."