Defender Thapelo Morena rifled in an 85th-minute winner in a deserved Group A victory to record a first win in six attempts over their continental rivals.
What makes the win more significant is that it comes against former coach Pitso Mosimane, who is the club's most decorated manager and is credited with transforming the club into perennial champions.
"Winning in Cairo was always our plan," Mngqithi said.
"We really wanted to win and in fact, I think the performance last year was stronger than this performance.
"We had many injuries this year and were worried in many areas.
"We knew the strength of Al Ahly and we lost a reasonable amount of starting players, from Dennis Onyango to Mosa Lebusa who scored at home. We also lost Erwin Saavedra, and two of our strikers in one week at home, Gift Motupa and Pavol Safranko.
"Otherwise, we're very excited to have won in Cairo but one must also say, it's a win for coach Pitso.
"He laid the foundation at this club, he's put his foot forward and always says this team still plays his football. So if Ahly lose and we won, it means he still won."