The Premiership champions lost 1-0 to Bucs in the first leg of their MTN8 semi-final on Saturday, with Daine Klate deciding affairs with a stunning 12th minute free-kick at Soccer City.
Baxter sprung a surprise by benching Musona, who has yet to score since returning to Naturena in the off-season, in favour of Majoro.
Majoro, who likewise is yet to open his account, struggled to make an impact in a poor opening period for Amakhosi, with Musona taking his place straight after the break. The Hoffenheim-owned striker was lively on his introduction but was guilty of wasteful finishing.
“We started with 'Major' (Majoro) because he understands how we play," Baxter told his club's official website.
"My rational was Knowledge would be better for us as a team coming off the bench. He is settling in well and will do well for the team this season."
The Briton added that his team are hurting following the defeat, which puts Pirates on the front foot for the return duel at Orlando Stadium on September 24.
“It is a bitter pill to swallow losing against archrivals.," Baxter said.
"The players in particular are very disappointed. This is football though and we have to focus on our next challenge."
Amakhosi next host neighbours Moroka Swallows at the same venue in the League on Tuesday night.