The Bafana Bafana midfielder is suspended after picking up two yellow cards in the Afcon Group D matches against Namibia and Morocco.
“To lose Themba, Themba has been playing very well for us and he is a very important part of the team that links sometimes in our transition, he does that very well," Baxter told the media on Friday.
"He is very creative in the last third and if you lose a good player like Themba, it is a blow but it also opens doors for other players like [Lebogang] Maboe and [Thembinkos] Lorch. They all want to put up their hands and get a chance."
The British tactician explained his side would try to match the Pharaohs in every aspect of the game when the two teams clash at the Cairo International Stadium in Egypt.
“Playing against the home nation is inspiring and knowing the Egyptian people, knowing their passion for football, knowing their expectations are very high, knowing they have some great players. I believe the pressure is going to be on them. It will obviously be a national disaster if South Africa beat them and for us, it will be very disappointing if we lose the game,” he explained.
“So, we will go into the game quietly believing we can cause an upset but knowing we have to play very, very well because this is a good Egyptian team and they will have massive support and one of the jobs we have to do is to try to quietly quieten the crowd by being a tough opponent than what the people think."
The former England Under-19 coach knows his charges will have to be at their best in order to eliminate Egypt, who are among the favourites to win a record-extending eighth title.
“This will be a great challenge and an inspiring challenge to be meeting Egypt. I think it is our job because the crowd will start with enthusiasm and it is our job to bring maybe some frustration into the mix and if we can do that and the crowd becomes a little bit impatient, the players will feel that on the field," he continued.
"We know that the home nation can be a good thing and that can also bring big pressure if they feel they are not pleasing that massive crowd. So that will be part of our job. We will play with no sense of we must, we will play with a lot of sense of we want. So if we can do that, I think it will be an interesting game. We will definitely give it a good shout on Saturday.
Baxter also revealed Bafana's defensive midfielder Dean Furman will face a fitness test after missing South Africa's last two games in Egypt due to injury.
“Dean Furman trained yesterday and he trained quite well. We took him out towards the end of the training as precautionary and we are waiting to see the reaction to that training today. The medical team will tell me the way forward,” he concluded.