Ndoro has 11 league goals from 16 outings this season, while Gabuza was unable to score in his first league start of the campaign against City at Cape Town Stadium.
Bucs salvaged a point, as Riyaad Norodien netted a last-gasp equaliser after his teammate Dove Wome's first-half opener was eclipsed by strikes from Roland Putsche and Lebogang Manyama.
"In football Costa is on the bench, Suarez is on the bench, Morata is on the bench. The problem in South Africa is people are surprised when you put someone on the bench," said Palacios, whose successor at Mayfair is expected to be announced this morning.
"Remember he [Ndoro] is our top goal scorer but in the last six or seven games he is not scoring. So to help him he needs to feel that there is someone there. I feel Gabuza did a very good job and the thing about strikers is that there is someone who can come in when a player has a situation and needs something to happen."
The Peruvian added: "According to the strength of Cape Town City they are aggressive and a physical team. Ndoro is more of a middle man in the box but Gabuza is more like a fighter.
"But this will help him to realise to score and this is a team and not about an individual. Ndoro was on the bench and never complained and even for us sometimes people say why I change the team.
"But because we need to give players' opportunity and this opportunity today, Wome scored and we make changes according to the game."