Johnson is adamant that Trundle has a big part to play at Ashton Gate.
"I spoke to Lee before the game and he understands my reasons.
"You bring people to the club because they are very important to the club, even if that means you have to leave them on the bench sometimes.
"In the end, these are the decisions you have to make and you stand or fall by those decisions as a manager. That's not Lee Trundle out, that's him being part of a 15 or 16-man squad.
"The one thing we can say about Lee Trundle is that he is going to play a massive part in our season. He's still very new to what we do here, but he can still be the hero for Bristol City."
He added: "I have to try and keep 20 players happy and I can't play all of them. The lads know why we change the team and we do speak to them first before putting things upon them.
"Once players are in my squad, they are all treated exactly the same. Everybody is equal here and I'll do whatever I have to do to make sure we stay at the top of this league."