The midfielder was replaced by Happy Mashiane midway through the second half, but the crowd at FNB Stadium expressed their dissatisfaction by booing the German mentor in protest of his decision.
However, Middendorp said while he respects the views of the Amakhosi supporters, Baccus had already indicated to him he wasn't sure if he would finish the match.
"You know, I understand the supporters. They are always right. For me personally, I think it’s a little bit of a disappointment. I took Kearyn Baccus out because at half-time he was already doubting if he could continue," Middendorp told SuperSport TV.
"Then I watched him and took responsibility and then the entire 20 000 fans are booing. I don’t know what to say. It’s the disappointment of the night for me but I’m happy for the brand Kaizer Chiefs and the team that they won these three points," he said.
Middendorp admitted the encounter wasn't easy for his charges because they only had three days to prepare for it after travelling to and from Durban in midweek.
"It is definitely a hard-working result. A game we’re used to playing but we definitely suffered after the Tuesday game [against AmaZulu] because we had three days [to prepare]."
Furthermore, the 60-year-old mentor explained why his team couldn't play beautiful football on the day.
"The injury that we had, I was aware of it that some of the players got knocks coming into the game. On the other hand, with a bit of a change in the second half, we were aware of it and we wanted to play a result-driven 45 minutes," concluded the former Maritburg United manager.