Dzeko went into Wednesday's friendly carrying a knock and he expected to be replaced at half-time during the clash in Innsbruck, which Egypt won 2-0.
However, Susic decided to keep Dzeko on the pitch for the full game and the forward was unhappy with the coach's decision.
"I came here with a niggling injury and Susic knew that, and he still didn't substitute me either at half-time, which was the plan, or after the break when I asked to be replaced," Dzeko said on his Facebook page.
"I don't know why he left me on the pitch for the full 90 minutes."
Dzeko also came under fire from some of the Bosnia fans after an indifferent display and the 27-year-old, who was Bosnia's top scorer in their successful World Cup campaign, says some of the supporters should be 'ashamed' of their behaviour.
"I wish to thank all fans who support me but the others should be ashamed because I am a born winner and always played my heart out for the national team," added Dzeko.
Susic also hit out at the fans for jeering Dzeko and blamed their defeat on missing several key players through injury.
"Dzeko didn't deserve so much criticism for a poor performance in a friendly, as anyone can have a bad day," noted Susic.
"Many players had a bad day but the fan reaction was unfair as we missed several key players through injury."