The Bafana Bafana midfielder made way for new boy Willard Katsande with about 10 minutes of regulation time remaining.
Chiefs' lack of creative spark in midfield after Tshabalala was taken off was noticeable, as Amakhosi went down 1-0 to their perennial rivals in extra-time to an Oupa Manyisa strike.
After the game, Vermezovic insisted that Tshabalala didn't deserve to play further than the 81 minutes.
"Look, in my team no-one is unchangeable and my philosophy is all Bafana Bafana players must always take responsibility.
"During the final we had a couple of players who didn't perform well and Tshabalala was one of them and that's why he came off.
"It doesn't mean he is not a good player, but he was not at his usual level, the real Tshabalala from Bafana Bafana," Vermezovic asserted.
He added: "I put in Katsande, because he has got a good shot and we were at that time trying to break down the Pirates defence, because it was impossible for us to beat them from around their box so we had to try from long range and I thought Katsande could do the job."
"Pirates' defence was compact and they played very good and that's why Siyabonga Sangweni was named man of the match. So, the idea was to get in a player who could hit shots from long range.
"I don't think the Pirates goalkeeper (Moeneeb Josephs) made many saves because their defence was good so a change was necessary.
Speaking to Football365.co.za afterwards, Tshabalala declined to comment on the substitution.
"I don't want to comment on that, but I do respect the coach's opinion. All I can say is that I'm disappointed of course with the result, but then again it is not the end of the world."