Dzeko played the entirety of Wednesday's 2-0 defeat to Egypt despite suffering from what he described as a "niggling injury", with the Manchester City striker claiming he asked to be brought off at half-time before the game.
The 27-year-old was also critical of certain sections of supporters who jeered his performance, but Susic responded on Saturday by denying any agreement with the player.
"There was no such agreement with Dzeko," Susic told Bosnian newspaper Dnevni Avaz.
"He wanted to come off in the second half but I left him on because, despite his claim that he was suffering from a niggling knee injury, the team doctor said he was match-fit with a proper warm-up.
"As long as I am in charge, Dzeko will play when (selected), while he won't be allowed to suggest or influence team selection in any way and that also goes for (captain) Emir Spahic, who also seemed to have his own ideas.
"I was a player too, but I never dared question the coach's decisions."
Dzeko is arguably the biggest name in Susic's squad and scored 10 goals in as many games during qualifying for the FIFA World Cup.
However, Susic warned the striker to expect more boos if he fails to deliver the goods for his national side in future.
"The present and the future matter more than the past in this business and the sooner Dzeko accepts that the better," he continued.
"People forget past merits very quickly and he can rest assured that they will jeer him again if he doesn't live up to expectations.
"On that note, the defeat and the performance against Egypt should be a hard lesson learned by Dzeko and the rest of the team."
