Musona will miss the big game on Saturday at FNB Stadium due to a shoulder injury he sustained when scoring in a Telkom Knockout quarter-final clash with Free State Stars last week, which Amakhosi eventually won 4-2 on penalties.
It is uncertain how long the Zimbabwean striker will be out for as further tests are needed to ascertain the damage.
"It is a blow to lose your top player," Baxter says.
"It is a shame for Knowledge because he has worked very hard to get himself fit and get to understand the way we play. The worst thing is this injury came at a time when he had just started firing so this is sad for us. However, this is a contact sport so such things should always be expected.
"He is definitely out of this weekend’s game and I know he will be out for a while but I will have to hear from the doctors about how long he actually will be out for once further tests are done.
"The initial scan showed that there is some damage which is something that we actually didn’t anticipate when he went down because he looked like he could still come back and continue," says Baxter of the loanee, who has scored in four of Chiefs's last six games.
The unavailability of Musona will come as a relief to The Bucs family as the slippery forward ran rings around the Pirates defence to score a memorable brace three years ago.
Meanwhile, Baxter confirmed that Siphiwe Tshabalala is in line to play having trained with the rest of the squad for the past two days.
Tshabalala was forced off the field with an ankle problem against Ea Lla Koto.