Teenager Meyiwa was dismissed in the 26th minute for a stomp on veteran attacker Daine Klate at Bidvest Stadium. Three minutes later Clever Boys striker James Keene netted the only goal of the match with a close-range header.
Wits will contest the final on December 2 at Princess Magogo Stadium with Bloemfontein Celtic, who edged Polokwane City 4-3 on penalties after 120 minutes of football produced a 1-1 draw at Old Peter Mokaba Stadium on Sunday.
“You could see with the early exchanges that we had all areas covered,” Komphela told his club's website.
“To suffer a red card in the first half in such an intense clash changed the game entirely. Besides that and to make matters worse, we let Wits score with a free header immediately thereafter due to a lapse of concentration.”
He added: “Our game plan was affected by this. If you check our substitutions, they were all intended to go for an all-out attack.”
Komphela introduced Gustavo Páez, Dumsani Zuma and Hendrick Ekstein in search of a way back but Amakhosi could not convert some promising chances.
“We came back strong in the second half,” Komphela pointed out. “Zuma had a one-on-one with Wits’ goalkeeper Darren Keet, Siphiwe Tshabalala hit the crossbar and Páez had a chance as well.
“We knew the game was going to be very tight and robust. Unfortunately we had to play most of the game with one man down. But still, I thought we contained them well and scared them a few times in the second half.
“Now that we are out of the cup, we have to focus our attention on the league. We will regroup and make sure we beat AmaZulu on Wednesday.”