Mkhwanazi has been out of action since May with a knee injury and the Clever Boys have missed him in their opening matches of the 2017/18 campaign.
Wits have conceded five goals in their three matches in all competitions so far and Mkhwanazi looks set to only make a return in October.
In his current squad, Baxter has selected captain Thulani Hlatshwayo, Mulomowandau Mathoho, Rivaldo Coetzee and veteran Morgan Gould to play in central defense.
If what Baxter said is anything to go by, then there's room for Mkhwanazi to be included in the squad if he can rediscover the form of last season. The 27-year-old former Mamelodi Sundowns player made 26 appearances in all competitions last season and scored five goals as Wits won their first ever league title.
"The only one I am certainly looking forward to seeing is Buhle Mkhwanazi. But he's got a long-term injury," Baxter said this week after announcing his squad.
Baxter will be hoping he does not get any more injuries ahead of the back-to-back 2018 Fifa World Cup qualifiers against Cape Verde.
Already goalkeepers Itumeleng Khune and Darren Keet have been ruled out and they have been replaced by Wayne Sandilands and Reyaad Pieterse.
Bafana will assemble on Sunday to start preparing for the crunch qualifiers.