Modise, an off-season signing from Mamelodi Sundowns, was set to make his Citizens debut in the 1-0 win over Polokwane City in the MTN8 quarter-finals at Cape Town Stadium on Saturday afternoon.
However, the 34-year-old's groin was acting up in the warm-up, prompting McCarthy to instead field Thabo Nodada alongside Roland Putsche in central midfield.
McCarthy explained to the media: "In training [on Friday] already his groin area started tensioning and pulling up, and he was feeling a bit of stiffness. So we pulled him out of training and he saw the doctor, and they said it was normal for his age and with the training pitch we train on; the pitch has gone a little bit as well. He just needed rest, a lot of ice and a massage and that's what he did. We didn't want to go the route where it could be fine but then he could damage it probably more and we lose him for longer periods in the season.
"With this one, okay it was an important game, it's a cup but I rather have Teko available for the rest of the season than forcing him to play [against Polokwane] and we get a good result, but he's missing a quarter of the season. It was one of the two, and we made the decision. He's feeling it, it's better just to rest.
"I'm not to sure if he will be back for the Wits game, but most definitely for Platinum Stars, Chiefs, Pirates. Those are the games we look to have Teko back because obviously for us to do well in those games, we need our general."
While McCarthy valued Nodada's industry in the engine room he felt Modise's composure was missed in a frenetic paced contest against Rise and Shine.
"Of course it does change the dynamics of the game. Obviously Teko is comfortable on the ball and he's our trigger, he's the one that distributes the ball to your Lebos [Manyama], [Sibusiso] Masinas, [Lyle] Lakays. Now with Teko being out of the team, we had to change the strategy a little bit so we brought in Nodada who is more high pressing and energy, but he is not as comfortable on the ball as Teko. So we were losing that part of the game. But yeah, so we didn't dominate the game as much as we would have liked to. That's what Teko brings us, he takes care of that ball like it's he's life, whereas Thabo's a little bit different."
The Bafana Bafana legend was nevertheless pleased to begin his tenure at the club with a victory after taking over the reins from Eric Tinkler in June. Tinkler also got off to a positive start at SuperSport United with a 1-0 defeat of Kaizer Chiefs last night.
"Overall I'm very happy, I don't have a lot of complaints. The defense was quite solid most of the time, but we must still learn to finish our opposition off when we have them on the back foot. We must go for the jugular instead of allowing them to see out 90 minutes when they still think they have a chance. I think we could have killed the game early on."
McCarthy's men will travel to Bidvest Stadium on Friday to take on Wits, who edged Golden Arrows 4-3 on penalties in a fiery MTN8 clash at the same venue.